Enemy of my enemy
by randomitegirl
Summary: During one of their trips, the Doctor and Clara find themselves in Samaritan's stronghold. After being forced to leave Clara behind, the Doctor turns to Team Machine for help in saving her. Doctor Who: pre-series 9 Person of Interest: 2 months after the season 4 season finale
1. Chapter 1

Head Notes: It has been a while since I have been able to post anything. I wanted to write a story that predicted what would happen next in regards to the Machine and Samaritan. But since I already know that anything I write will most likely be disproved, I decided to just have fun with it. So I decided to do a crossover with Doctor Who. Also I want apologize to all those who are following my Monk story. I have officially hit writer's block for that one so it is on hiatus until I figure out what to do with it next.

Enemy of my enemy

Chapter one

"So where are we off to this time?" Clara asked, her eyes flashing in anticipation of their next adventure.

"Well, there's Trighton, the civilization completely built underwater, or we could visit the planet of the Cribbon race. They use their telepathic field to predict and anticipate the needs of any individual. Which comes in very handy for their very own planet-owned restaurant famous throughout the galaxy. Best restaurant in the universe, hands down."

"Well then who am I to miss out on the best restaurant in the universe?" Clara decided.

"I thought you would say that." The Doctor stated, grinning as he threw the gears into place.

The TARDIS's melodious atmosphere flashed and groaned happily. Clara had had no idea how much she had come to love that sound until she'd spent time without it. It had only been a few weeks between the time Danny died and when the Doctor came back for her but those few weeks with no distraction, no time and space adventures, and no excitement outside of teaching had nearly driven her mad. And to think she had almost lost it.

When Danny had died so suddenly, she'd been so desperate to save him, so impulsive that she had taken her anger and confusion out on the Doctor. The only two men that had ever served any real purpose in her life, and in her rash judgement she had nearly lost them both. The TARDIS groaned as its gears wound down, landing with a thud.

"What's the weather like there?" Clara wondered. "Is it hot, warm, or cold?"

"It's fine," The Doctor insisted, opening the doors.

The sight that met him outside the TARDIS stopped him in his tracks. A windowless room crowded with servers and a variety of computer equipment. The sliding door on the other side of the room with an electronic lock however, told him that this wasn't a normal server room. He didn't know where he was but it wasn't at the restaurant. He doubted that they had even left Earth.

"What's going on, Doctor?" He heard behind him as Clara followed him out of the TARDIS. "This isn't the restaurant, is it?"

"Ah! You noticed that, did you" He stated sarcastically. "Yes, I think it's a fair assumption to say we missed the restaurant. I don't think we've even left Earth.

"Where are we?" She asked.

"Geographically," the doctor began, moving around the room. "Somewhere in North America. Possibly the East Coast. Specifically, I have no idea."

He took out the Sonic Screwdriver and scanned around the room. "We are in some kind of server room."

"What?"

"Where businesses store their computer systems," he explained.

"Okay, Doctor, that's all fine and everything, but can we not just go?" Clara nagged. "We did agree to go to the restaurant."

"We can't. Not until I've figured out what this is," he insisted, continuing to scan the room.

"You just said that this was a server room," Clara reminded him impatiently.

"It's not a normal server room," he hushed. "I don't know what it is but there's something different about it. Like it's linked to something bigger."

"Like what?" Clara wondered.

"I don't know," he breathed. "But one thing's for certain. We are never going to find out by staying in here." He said as he held the sonic to the electronic lock.

The door slid open and the Doctor and Clara stepped out into the cool hallway.

"So, what do we look for?" Clara asked.

"Anomalies," he answered. "Anything that sets this place apart from any other."

Neither of them noticed or cared that there was a security camera overlooking the entire hallway. Even if they had, neither of them would know that the camera's observations were being directly uploaded into the brain of an Artificial Intelligence. Including the observation of two unidentified intruders roaming the halls where no unauthorized persons were allowed. The two intruders silently moved down the hall unaware of the danger they were in.

The Doctor suddenly stopped in his tracks.

"What is it?" Clara whispered.

"Shush!" He hissed.

He raised the sonic screwdriver into the air. Just as he thought. There was a stream of silent communication being broadcasted throughout the building. He couldn't hear what they were saying, but he didn't like their chances.

"I think we might have company," he whispered to Clara.

No sooner had he said those words that alarms in the building began blaring loud and sharp in their ears. The Doctor and Clara instinctively covered their ears at the sudden racket.

"Run," the Doctor ordered, turning back toward the room they had left.

His side burned as he bolted down the hall. He heard Clara behind him, panting to keep up with him. Just then he heard a gunshot and a bullet whistled past his ear. Of course, what else could it be? He raised the sonic as he drew nearer to the door in front of the TARDIS and the locks disengaged, sliding the door open. Just as he got to it, it started to slide close again. With a desperate leap of energy he dove through the door just before it slammed shut.

"Doctor!" Clara called after him, and desperately pounding on the door.

"Hold on!" he called, sonicing the door. The door opened only halfway before forcing its way closed again. "No! No!" He boosted the sonic but it only slowed the door.

He looked past the crack in the door to Clara's panicked eyes.

"I'm sorry," he said. "I can't open the door. Some very strong technology is interfering with it."

Clara looked behind her and back at him. "Then go." She insisted, the fear in her eyes palpable. "They'll be here any second."

"They will kill you," he stated.

"I very much doubt it," she said.

"Why?"

"Because, my friend will not rest until he finds a way to save me in the nick of time," she said, smiling through her fear. "Now go."

The Doctor gave one last look at Clara.

"I will find a way to save you." He said even though he was sure there was no way.

He released the sonic and the door clamped shut.

XxXxXxX

Clara looked after the doctor as long as she could before the door finally closed. She knew there was no way out for her. As soon as the men with the guns found her she was as good as dead. But the look in the Doctor's eyes was already painful. She gave him hope that he might be able to save her, because that was the only way she'd get him to leave. Sure enough, a few moments later she heard the TARDIS powering up and the sound faded just a few seconds later. Just as the stampede of feet rounded the corner to where she was.

She turned to face them, determined to remain defiant to the end. They were going to kill her anyway. She might as well go out with a bit of dignity intact. At least a dozen people, men and women, surrounded her pointing high-powered firearms at her.

"Now, now, let's all calm down," an older gentleman said in a British Accent, making his way through the crowd. "Now young lady, where has your friend gone to?"

XxXxXxX

Harold Finch fumbled with the briefcase again. Working desperately in the underground subway base, he had managed to give the newborn Machine new capabilities but he wouldn't be able to see the full result until he switched it on, at which point Samaritan would detect it. He and Root had tried small test runs. Root had likened it to giving a child permission to walk around the block. At first it couldn't do much more than observe. But with each test run, they ran different simulations of the different functions. Testing out its abilities one at a time. Today they would expand its horizons. They were going to test its ability to see and act on information it perceived. Dangerous, but necessary to let it grow any further.

"Are we ready?" He asked, turning stiffly to her.

"Time to resurrect god," she whispered seductively.

Harold flicked the switch and the lights flickered to life. Root closed her eyes as the information the Machine processed coursed through the Cochlear implant into her mind.

"What does it see?" he asked.

"Give her a minute, She has to sort through it all," she hushed. "Hold on, She's seeing something. Someone."

"There are 7 billion people in the world," Harold pointed out.

"She says there is something different about this man," she reported. "I'd almost say She was excited to see him. Like She can't wait to meet him."

Harold narrowed his eyes, puzzled. "Who?"

"Excuse me, Harold," she pardoned. "She wants me to meet him for coffee."

XxXxXxX

The Doctor stood silently in the TARDIS ignoring everything around him. The fury building in his chest as the incident replayed in his mind. Whoever they were, these people had most certainly killed Clara. In most cases, he was willing to forestall judgement on intelligent beings. But that same courtesy did not extend to those who even touched his friends. In fact, now that they had done so, he would make absolutely certain that whatever this company was, it would never hurt anyone again. Even if he had to burn the building to the ground. And those that had killed her would most definitely face retribution. But first things first, he had to figure out what that place was and how to exploit their weakness.

Before he could make a move, the TARDIS phone rang. That sound had never been so welcome as it was now. For a brief moment, hope rose in his chest. If it was Clara, it meant she was alive. And if she was alive he still had a chance to save her. He leaned out of the door and answered the phone.

"Clara?" he called.

"Seven. Six. Five. One. Broadway." It was a computerized voice. Like different audio clips of people talking.

"Who is this?" he asked.

"Seven. Six. Five. One. Broadway." The voice repeated. Was that all it could say?

"What will I find there?" he asked.

"Help. Needed. Doctor." The voice said.

"I'll be right there," he replied.

He didn't know what the voice was. If it was going to help him, trap him, or anything. But right now he needed information. Even the smallest detail might help him save or avenge Clara. He launched himself into the TARDIS and fired it up. It landed with a thud a moment later.

Straightening his collar, he exited the TARDIS into a busy street. He didn't know what he was looking for so he kept his eye pealed for any anomalies.

"Excuse me," someone tapped on his arm. She was a head shorter than him and dressed in black. Even her fingernails were painted black. But the most obvious thing about her was the coy smile playing on her lips. Like she was holding in some great secret. "I'm supposed to take you for coffee."

XxXxXxX

End Notes: So I've already written out most of this story so I will be able to post it on a more regular basis. But for now, what do you think so far?


	2. Chapter 2

Head Notes: Back again. I loved writing this chapter, specifically the interaction between the Doctor and Root. And I hope it is an enjoyable read. Enjoy!

Chapter 2

Clara sighed once again as her eyes wandered the walls of her prison. She'd been surprised when the old man had spared her life. At first she was relieved. But after staring at the walls for so long, she was growing bored. She didn't even know what time it was. The men had taken and destroyed her phone so there was no chance she could send a message to the Doctor or call for help. And the clock in the room had been removed. She had a bed and some water in a jug, but not much else. There wasn't even a window she could look out of.

Finally, the lock on her door started beeping and the door opened. The old man came in with a delightful smile on his face.

"Good morning, Miss Oswald," he greeted in a British accent.

"Why are you holding me here?" she asked. "No, hang on, better question: What is this place? You've got a private army, an insanely quick response time, and, judging by the way you haven't killed me yet, you need this place to be kept private, don't you. That's why you haven't killed me yet. Because my friend is out and you need to find him, don't you?"

The man didn't make a sound as she spoke, letting her work things out on her own. He almost looked impressed as she moved from one conclusion to another.

"A bright young lady is always a beacon of light in this dark world," the man replied, smiling. "But you're not the usual bright young lady. Your records show that you are already a school teacher at Coal Hill School in London. It's the middle of the school year, Ms. Oswald. What are you doing on the other side of the Atlantic?"

"Funny," Clara said slowly. "That's exactly the question I was going to ask you."

The old man gave an amused smile.

"So, where is your friend?" He asked. "How can we find him?"

Clara laughed. "You think you'd be able to find the Doctor?" She smiled. "Good luck, because he never stays in the same place for long."

"I sincerely hope you change your mind," he said, turning to leave. "Your stay with us will be much more comfortable if you cooperate."

"Never," Clara hissed.

"Very well," he said, closing the door behind him.

XxXxXxXxX

The Doctor watched as the woman sipped her coffee savoringly, his own coffee practically untouched. She had chosen a shop with an outdoor patio, the umbrella on top of their table providing shade. She put down her cup and looked across the table at him.

"Who are you?" he demanded.

"Well, Doctor, you can call me Root." She answered.

"How do you know my name?" he wondered.

"My boss has been telling me all about you. She's had to go quite a ways back to put all the pieces together and now, She's kind of a big fan of yours. The different faces throws Her off sometimes, but one thing always gives you away."

"And what's that?" he asked.

"The blue box," she whispered intriguingly. "She says it took her years to figure out how all those faces were one man. Until one day She found footage taken from a hospital where she saw one version of you die on the operating table and another stand up and walk away." She shook her head disapprovingly. "Humans can be so disappointing, can't they, Doctor. Although, I guess, in their defense, how could they know?"

"Know what?" he whispered. Though he suspected what she was going to say.

"That you're not human." The coy smile playing on her lips unsettled him. How did she know all this?

As if she could read his mind, she continued. "Your medical records from the time you served as the scientific adviser for the Unified Intelligence taskforce. They report that you have two hearts and that your blood type is not matched to any living creature native to Earth. We must be like ants to you."

"So since you know all this," the Doctor interrupted. "How are you going to help me? What is your boss going to do?"

"Well, first of all, She wants you to know that your friend Clara is alive and safe for now. The people that have her haven't killed her."

"She's still alive?" he breathed in relief. A relief that simultaneously transformed into worry. "Where is she? How are we going to save her?" the Doctor interrogated, rising from his chair.

"For a man who travels through time and space, you seem a bit short on patience," she remarked.

"Shut up! Just shut up!" he hissed, leaning over the table. "My friend is trapped in an unfriendly place with people armed to the teeth with guns. People who I have no doubt will kill her the moment they can find no use for her. And if that happens because we spend too much time criticizing my bedside manners, then you'd better be very, very careful how you speak to me."

"Relax," she smiled, meeting his stony glare with the same coy smile. "My boss wants to help save her. The problem is there isn't much we can do without your help."

"What do you need?" he growled.

"The people who have your friend are ruthless and not to be underestimated," she whispered softly. "The only way we can save your friend is to destroy them once and for all. We have a team working on something that will help with that, but my boss says that with your help, our chances of actually succeeding improve by ten percent."

"So basically, you'll help me if I help you," he summarized.

"If it makes you feel better, we are under the same predicament you are," she smiled coyly, reaching across the table to grasp his hand. "Are we ready, Doctor?"

XxXxXxXxX

Claire Mahoney walked through Samaritan's new base. After the last four months, they had regularly changed the base location, usually lasting about a month and a half or so before moving on to the next. She didn't know exactly why they changed bases so often, but she figured it was a way for Samaritan to remain discreet and undiscovered.

Frankly, she didn't know why they were keeping it a secret. All the amazing things Samaritan was doing, the work it was doing educating children, making sure they could fight their way out of a life of poverty, and planning a way to feed not only children here in America, but in other third-world countries. A program so advanced it was finding ways to solve all the problems humanity had created for themselves. If it was up to her, she would shout from the rooftops about the brilliance and passion of this amazing A.I. But for now, Samaritan wanted to remain a secret.

She caught a glimpse of Mr. Greer just as he exited a room. He put in the lock code and the deadbolts fastened in place. It wasn't a room they used very often and they only locked the doors when the room was storing something valuable. And ever since he'd ordered her shot on a rooftop with no guarantee of survival, she'd found it difficult to trust him.

"Mr. Greer," she called.

"Good morning, Claire," he beamed, flashing a grandfatherly smile. A smile she had come to distrust.

"What's in there?" she asked pointing to the room he had just left. She tilted the blinds on the door to see a woman about her age. "Who is she?" she asked.

"We don't know," he answered. "Samaritan detected an intruder and saw this young woman and an older gentleman loitering in the hall. The man disappeared and this young lady remained behind. And she has made it clear that she will not cooperate on her own accord."

Claire didn't like how this was looking. Greer was insane and really lacked imagination. There was no telling what he would do to the woman in order to get answers.

"What if I talked to her," she suggested.

Greer turned to her puzzled. "You think she'd talk to you?" he wondered.

Not knowing whether that was an insult to her abilities or a genuine concern, Claire continued.

"She is practically my age," she pointed out. "She may connect better with someone closer to her age. Then I might be able to establish some rapport."

"Perhaps you're right," Greer decided. He put in the lock code and the locks clicked again. Claire turned the handle and walked inside.

XxXxXxX

Clara glanced at the girl that entered her prison. What, did they think she'd betray the Doctor to someone her age?

"Hi," the girl began. She was American. "Sorry about him. He tends to go to extremes to keep this place secret."

"What is this place?" Clara asked.

The girl looked at her confusedly.

"You mean, you don't know?" she asked. At Clara's head shake, she took a deep breath. "Then why are you here?"

"Wrong place, wrong time," she responded. "Happens quite a bit actually. Where am I?"

The girl looked back at the door, then up into the corner. After a moment, she turned back to Clara.

"I suppose you deserve to know," she decided. "I know I'd like to. Have you ever noticed cameras? Like in stores, or movie theaters or on street corners?"

"Of course I have, I'm not blind," Clara answered.

"They aren't either," the girl said.

"Meaning?"

"Well, all the video information they collect, on any person at any time is accessed by an A.I." The girl explained. "The most powerful artificial intelligence with an almost god-like omniscience. It can find the answer to any question. The solution to any problem."

As the girl continued with her description, her countenance brightened.

"And its name is Samaritan," she finished.

"Okay, an Artificial Intelligence in 2015," Clara repeated. "Why hasn't anyone heard about it?"

"I think Samaritan wants to focus on helping humanity first," the girl answered. "It's got programs in place to solve hunger, power corruption, and war. All these problems that humanity made for itself can be solved."

From what the girl said, this Samaritan was similar to the Doctor. Flying around trying to solve problems too big for humanity to fix itself. With one significant difference: the Doctor would never use guns the way these people did. He wouldn't even allow people around him to use gun like this. Still, this girl, whoever she was, might just be her only way out of here. She seemed nice enough.

"What was your name again?" Clara finally asked.

"Claire," she answered. "Claire Mahoney."

"That's funny," Clara smiled. "I'm Clara."

The girl smiled for the first time since she entered the room. She sat down on the end of her bed.

"So, I've told you a little bit about me," Claire said. "What about you?"

"I'm a school teacher. Year eight to Year Ten," she said, careful not to give anything about the Doctor.

"A school teacher? Really?" Claire repeated. "I am too. Well kind of. I provide technical support at some Charter schools."

"Cool, how did you get started on that?" Clara asked.

"It was Samaritan's idea," she replied. "The education system is failing in America. And let's face it Common core is just a short term fix to a long-term problem. Like putting tape over a hole in a dam. Samaritan might not be able to fix the students' financial situations, but it has found a way to help children educate themselves so they can build a better life for themselves when they are older."

"No greater way to change the world than to educate a child," Clara agreed.

"Then why aren't you there now?" Claire asked. "What brought you all the way to America in the middle of the School year?"

"It's just where the Doctor landed," she blurted out before she could stop herself.

"Doctor who?" Claire asked.

"Nothing," Clara blurted out. "Out! Get out, now!" How could she have let her guard down so easily? "You are going to have to try harder if you think I'm going to betray the Doctor for the sake of conversation."

She furiously turned away from Claire, refusing to look at her. She listened as Claire made her way to the door and paused before leaving the room.

Oh, how could she be so careless? She might have given everything away. Might have given them everything they needed to know to find the Doctor. The Doctor was hard to find, but if Claire was telling the truth and Samaritan had eyes everywhere, how long could he hide from them?

XxXxXxX

End Notes: The Machine is a Whovian. Need I say more?


	3. Chapter 3

Head Notes: Back again. Enjoy!

Chapter three

Claire stopped at the door to look back at Clara. The warm smile that had melted her features was gone in an instant. Quickly replaced with a furious cold rage the moment she had slipped and mentioned her friend. Clearly a friend she was very close to and very defensive about. After a moment, she turned the handle and walked out of the room.

Moving to the main control room, she stopped as Greer called her name.

"Did she give you anything?"

"Only that her friend is a doctor," Claire answered. "But that's when she panicked and yelled at me to get out. She didn't even give his name."

"Her friend is a doctor?" Greer repeated, faint worry lines creasing his forehead.

"Is that important?" Claire wondered.

Mr. Greer lifted the blinds on the door and gave Clara a good long look.

"Samaritan is concerned." He began. "It has been spotting a pattern over the past few months, a blue box with a man inside calling himself 'The Doctor.' If Miss Oswald is a friend of the Doctor, then he must be found."

"What will you do?" she wondered.

Greer glanced at her for a moment before turning his attention back to Clara.

"We will have to interrogate her," he said simply.

Claire stifled a groan. If only Greer would realize there was more than one way to get information. Crude tactics and intimidation would only get so far. People were more willing to talk to people who garnered trust. People who became a confidant; someone they could share intimate details with. She imagined Greer went straight to interrogation because it was faster. He wasn't patient enough to try plain old human interaction. But he got results and that was what he cared about. That was why Samaritan put him in charge. Something she'd learned over the past year, Samaritan didn't care what methods were used as long as they produced results. Maybe one day Samaritan would put her in charge and she could change the methods and tactics for more efficient ones. But until then, Greer was the superior.

"Fine," she said with an exaggerated sigh. "With one suggestion. When you are not busy interrogating her, I want to be with her; talking to her."

Greer looked back at Clara as he thought about it.

"Perhaps a wise decision," he agreed. "Though for now I think you should give her time for herself."

"Alright," she said. Suddenly noticing the clock, she realized that she was going to be late for her next job if she didn't leave now. "I need to go to my next shift. See you later."

Greer wished her a good day and watched her leave. As soon as she was out of sight he spoke. To appearances sake, it would seem like he was talking to himself. But the words were intended for his A.I. superior.

"She's starting to ask questions," he said. "Starting to doubt authority. What should be done with her?"

He drew his phone out of his pocket as Samaritan calculated its options. After a moment, his phone beeped.

OBSERVE. TAKE NO ACTION.

"Very well," he breathed, slipping his phone back in his pocket.

XxXxXxX

Root stepped out of the restaurant quickly followed by the Doctor. Honestly, she hadn't known what to expect from him. He was definitely a fighter. He would never be the kind of person to lay down and die. And he had no patience for small talk with his friend in danger. He seemed even less patient with her. She was sure that the only reason he had agreed to work with her was in order to save his friend. As for her, she genuinely enjoyed his company.

He looked to be about Harold's age (though she had no doubt he was much older than she could imagine.) and had the same dress style. A dark slender suit with a vest over his white shirt. But the most obvious things about him were the eyebrows and the thick Scottish accent. The eyebrows themselves were worth mentioning independently. By themselves, they could transform the entire look of his features. Which became really obvious when he'd leaned over the table to threaten her. The Machine was turned off now. Harold had probably switched Her off to avoid discovery. And now, she needed a place to hide the Doctor. Once Samaritan realized who he was and captured him, all their advantage would be lost.

"Your TARDIS can go anywhere? Fit in any place, right?" she clarified.

"Yes," he grumbled. She smiled as the picture of him scowling behind her entered her mind.

"Good. 'Cause I need you to take us to a specific address." She said.

At that, the Doctor growled and swung her around to face him. Root panicked for a moment as his cold, unforgiving eyes glared into hers.

"No. No. No." he growled. "You don't get to order me around. You don't tell me what to do or where to go. I agreed to help you but I never agreed to become a little pawn that you say, 'oh, go over there,' or 'go sacrifice yourself here.' If you want my help you will tell me what is happening."

"None of that will make any difference if we don't get off the street," Root said calmly. "And if we are going to work together we need to find somewhere more private."

She watched his eyes as he contemplated what she said.

"And work on your trust issues," she added.

His nostrils flared at her comment, but he controlled himself.

"Now, your TARDIS?" Root reminded him.

"This way," he said, making a point of leading the way.

He seemed to have an obsession with being in control. Although, since he had at least a few hundred years of experience she supposed that was understandable. They made their way through the crowd and the Doctor took a key out of his breast pocket and unlocked the Tardis.

The Machine had warned her that the TARDIS was bigger on the inside, but the sight of it still overwhelmed her. The dark lighting with orange and blue shades augmented the stairs and bookcases that filled the space. The console in the middle, laden with hundreds of buttons and levers, connected to the ceiling by a tall translucent column with three circular levels, each one slightly larger than the one below it. It was beautiful. The closest humanity would get to any kind of heaven.

"Well, aren't you going to say it?" the Doctor asked.

"Say what?" Root asked.

"That the TARDIS is bigger on the inside than it is on the outside," he boasted with a satisfied grin which faded a moment later. "Let me guess. Your boss told you."

Root replied with a smile of her own. "You're catching on."

"So what is the specific address you want me to take us?" he asked.

Root gave him the address of the safe house and he typed them into the TARDIS and fired it up. He pulled a lever and the TARDIS began groaning and wheezing. She smiled as the column in the middle moved up and down. Taking her phone out of her pocket, she texted Harold to meet her at the safe house. The TARDIS landed with a thud, just as she slipped her phone back in her pocket.

"Are you going to tell me where it is we've landed?" the Doctor asked.

"Like I said, a private place to meet," Root answered, opening the door of the TARDIS. "There's food in the pantry and tea in the cupboard. Help yourself."

XxXxXxX

The Doctor followed Root out of the TARDIS into an apartment room. It was bigger and more open than Clara's room, but had less furnishing. He'd guess that no one formally lived here. The door had a keypad next to it, indicating that it was fitted with an electronic lock.

He'd only known Root for a half hour and already he didn't like her. The smug smile on her face as she revealed private details of his life didn't help. It was obvious she wasn't attached to UNIT so there was no plausible reason for her to know so much about him. But that wasn't even the most unsettling thing about her. The coy smile and the smug look in her eyes hinted that she was hiding something. Something big. Something that might help him save Clara. Yes, he sometimes hid things from people, but it was his job to be mysterious and have all the facts. But she was hiding information that could help him save Clara. If Clara died because he didn't have that information, it would be Root's fault. Plus, there was that text she had sent. The way she did it suggested that she had been trying to hide it from him. Hoping he wouldn't notice. But the old Time Lord noticed almost everything.

She plopped herself down on the sofa and made herself comfortable.

XxXxXxX

End Notes: So, likes? Dislikes? Any suggestions for better writing?


	4. Chapter 4

Head notes: I apologize for not posting anything yesterday. I was extremely busy. Also, I don't know if I will be able to post anything the next few days since I am traveling out of town and I am not sure if there will be WiFi. But I made a goal when I started this story that I would have it finished before season 5 started and I am almost there. But for now, here is chapter four. Thank you and enjoy!

Chapter Four

Harold made his way to the safe house as quickly as he could. The cryptic text Ms. Groves had sent him stressed the need for haste. Curiously, it also instructed him to bring the Machine. He hadn't heard anything from her since they first turned it on earlier. She hadn't even told him who the Machine had seen. She had simply instructed him to keep the Machine running and he had for as long as he felt comfortable. After thirty minutes, he became worried that Samaritan would notice and had switched it off.

He didn't know what trick Ms. Groves had up her sleeves, but he hoped it would prove more efficient than their previous attempts. He pulled up next to the safe house and grabbed the briefcase before stiffly easing his way out of the car.

XxXxXxX

The Doctor stirred in the twelfth teaspoon of sugar in his tea and walked back into the front room. Root had taken to entertaining herself with her phone and glanced up at him as he walked back into the room.

"Enjoying the tea?" she asked, making small talk.

"I've had better," he snapped. How he hated small talk. "So are you going to introduce me to that amazing boss of yours?" he asked.

"Eventually," Root assured. "She prefers it when we take things slow."

"We don't have time to take things slow," he insisted. "My friend is still in danger and her chances are dropping every second we waste talking."

"Believe me, my boss wants to save her just as much as you do," Root insisted.

"Then what are we waiting for?" He demanded. "Why are we sitting here talking?"

This time he didn't wait for an answer.

"Forget it," he said, standing up and making his way for the door. "If all you are going to do is sit around, I will rescue her myself."

"Doctor, no," Root said, panic rising in her eyes. She cut in front of the Doctor, with her back to the door. "They will kill you before you even have a chance. And you won't do Clara any good if you are dead."

"It's better than doing nothing," he said, pushing her aside and taking out the sonic screwdriver.

"Just give me time," Root insisted, cutting in front of him again.

"How much time?" he growled. "How much of Clara's time do you want me to waste?"

"Two minutes," she replied.

Just as she answered the locks on the door beeped and the code was put in. The door opened to reveal a short man in glasses carrying a briefcase. He froze in mid-step when he met the Doctor's eye. For a moment, the man looked trapped as he took him in.

"Relax, Harold," Root said, the coy smile back on her face. "He's here to help."

The man, Harold, looked back at him. After a moment, his eyes scanned the room and fell onto the TARDIS.

"How did that box get in here?" he puzzled.

"Gee, I wonder," the Doctor began sarcastically. "Maybe we smuggled it in through the door that's too small for anything wider than a man. Maybe we folded it up and squeezed it inside."

The man took in his answer with a confused and puzzled look on his face.

"Boys, play nice," Root reprimanded them as if they were children. "Harold, this is the Doctor and there's quite a bit you should know about him."

"You know what, I find it easier just to do this," the Doctor said, moving to the TARDIS.

"This is my time machine," He said, throwing the doors open and letting Harold come and take a look. "It also travels in space. I can go anywhere, anytime, take a quick tour of the Herculeous Galaxy and be back in time for tea."

"Oh my," His eyes widened as he took in the immense size of the room. He stepped inside looking around the console room like a boy in a candy store. "How in the world is this possible?" he wondered, stepping outside to double-check the size of the outside.

"It's not possible in your world," the Doctor answered.

"My world?" Harold repeated. So he didn't know about him. Why did only Root know? Was he kept out of the loop as well?

"Dimensional engineering is never achieved on Earth. You lot manage to invent vortex manipulators and space ships larger than an ocean liner, so you can travel through time and space. But a feat like this is never accomplished by humanity."

Harold stepped inside the TARDIS again, setting his briefcase down, before giving himself a more in-depth tour of the console room. He moved around the room, taking in every little detail with fascinated glee.

"Oh my goodness," he breathed as he stopped in front of the bookshelves. Taking a book, he turned to face the Doctor.

"This is a first draft, first edition copy of Chekhov's first published story," he said stunned, holding it up for the Doctor to see. "I've been looking everywhere for this. How did you find this?"

"Easy," the Doctor said. "I went back in time, bought a copy. I even got him to sign it for me."

"No way," he breathed, flipping to the front page. Pure excitement exploded in Harold's face as he beheld the words penned by the author's own hand.

Despite himself, the doctor couldn't help but smile at Harold's expression. The man was definitely cultured with a good taste in literature and style. He also gave off an unassuming impression. In fact, if the Doctor hadn't noticed the briefcase or the lock on it, it would have been very easy to underestimate him. He also gave off the impression that he was used to keeping secrets from others. But in a way that was different from Root. In fact, he had the exact opposite effect Root did. The Doctor had a feeling that he and Harold would get along just fine.

"Alright Harold," Root called. "It's time to talk."

Harold gave one last look at the book before shelving it and exited the TARDIS.

"So, if you're an extraterrestrial time traveler," Harold began. "What are you doing here?"

"My friend was captured," he answered. "She," he continued indicating Root. "Has yet to tell me exactly what we are going to do."

"What do you mean?" he asked.

"She offered to help me rescue my friend if I help you lot," the Doctor explained.

It took a moment for the Doctor to realize that Harold was no longer next to him and he looked back. Harold was looking at Root as if she had betrayed some grand promise. An expression that bordered between disappointment and disbelief.

"Ms. Groves," Harold called, his voice slightly higher than it had been. "May I speak with you in private?"

"Are you sure that's a good idea?" she asked. "The Doctor here isn't a fan of secrets."

"Kitchen, now," he said, his tone leaving no room for argument. "If you'll excuse us." He pardoned.

XxXxXxX

Harold stepped into the kitchen, waiting for Root to follow. How could she be so reckless? So careless? To gamble an innocent woman's life for the sake of an advantage.

"What's got your kite string in a knot?" Root asked.

"Ms. Groves," he said, lowering his voice in case the Doctor was listening in. "What on Earth are you thinking?"

"That we have an alliance with possibly the most powerful man in the universe," she answered honestly.

"An alliance that doesn't have to be based on dangling a carrot," he reprimanded. "Where is his friend?"

"They accidentally got themselves on Samaritan's radar and he was forced to leave her behind," Root explained.

"Samaritan?" Harold repeated. "That's who has his friend? Ms. Groves, you know how unsure that possibility is. There is no way we can guarantee that we can save her. And this man, the Doctor has no obligation to step in just because we are short-handed. We can't put an innocent man in danger for the sake of an advantage."

"Look with or without us, he is going to try to save his friend," Root reasoned. "And the Doctor and I agreed that we both stand a better chance of succeeding in our goals if we worked together."

Harold always found it irritating that Root could find an answer to every argument he posed. It always felt like she could get anyone to agree to anything.

"And if it makes you feel better," Root continued. "The Machine says our chances improve with his help."

"Fine," Harold reluctantly agreed. "But we can never tell him about the Machine."

"Is that a good idea? Keeping him in the dark?" Root wondered.

XxXxXxX

The Doctor watched as Harold and Root walked into the kitchen. Stupid, primitive pudding-brains! They asked for his help. How was he supposed to do that if they kept things from him? No matter. He could find information on his own.

The briefcase Harold brought with him obviously contained something important. Easy enough to deduce by the lock on it. He looked to the kitchen to make sure they weren't coming back, but they were too engrossed by their discussion.

Taking out the sonic screwdriver, he approached the briefcase leaning against the TARDIS and knelt down. He tripped the lock easily. Well, relatively easily considering that it was protected by the most advanced defense for this age. He carefully opened the briefcase, letting the half closest to him rest on the floor.

"Ohh, ohh," he sighed, taking in the sight that met his eyes.

He didn't know what it was yet but it was brilliant. Thirty-eight state of the art storage ram chips. The latest available storage technology going by the year. They were storing something huge. After a moment studying the architecture, he flipped the sonic screwdriver open and scanned it.

The ram chips were storing some kind of code. Computer code that went well beyond twenty-first century Google. It was so advanced he was tempted to assume it was alien technology. But no, it was human made. Impressive work for a human, especially in this age of primitive technology. But it was still too hard to see exactly what it was.

Whatever it was, it couldn't be turned on without a connection to an external source like a computer. He'd have to wait until he had access to one before he could work out what it was.

Closing the briefcase, he locked it back up and put leaned it back against the TARDIS. Clearly whatever that code contained, it was a big part of Root's plan. If he wanted to save Clara, he had to figure out what was in that code and what it was for.

XxXxXxXxX

End Notes: So what do you think? Do I have the characters down alright? Is the story flowing okay so far?


	5. Chapter 5

Head Notes: Sorry it took so long. I got back yesterday after spending a lot of time with family. But here it is. Enjoy!

Chapter five

Clara sighed out of boredom for what had to be the thousandth time. Her captors hadn't given her access to any kind of human interaction after Claire had left. She knew in her mind that it was a method to isolate her; make her suggestible to interrogation. But she couldn't deny its effectiveness. Not able to take it anymore, she stood up out of her bed and walked around the room. The room was too small to allow much room for pacing, but it was still better than sitting on the bed and staring at the walls. And at least it gave her the opportunity to stretch her legs.

Okay, the Doctor, what would he do now? There were so many different answers to that question. One thing he always said was that getting captured was the quickest way to figure out anyone's plans. What plans did this Samaritan A.I. have? She couldn't ask the computer directly, but she had enough experience with interrogation to turn the tables and get information from the captors without giving her information away.

Her attention turned to the door as the lock began beeping. The door opened revealing the old man and three others.

"Wow, about time I had some visitors," Clara commented.

The old man smiled at her remark as the three people took positions around the room.

"I suppose after 8 hours of solitude any company is better than no company at all," he returned. "Have a seat, Ms. Oswald."

Clara scanned the room, taking in each eye as they watched her sit down on the bed. None of them looked particularly friendly.

"Ms. Oswald, how do you contact your friend?" he asked.

"What, you think I'd tell you?" Clara remarked. "Don't be daft. And you're an idiot if you think you can find him."

"This will be a lot easier for you if you cooperate," he warned.

"It'll be a lot easier for you if you let me go," she returned. "Because if you don't, you won't have to find him. He will find you. And he will burn this place to the ground if it means he can save me."

"Very well," he sighed. Turning to the others, he said, "Proceed."

Two men approached her on the bed and pushed her back on the bed.

"What are you doing," she asked, beginning to panic as she tried to fight them off. But the more she fought, the tighter the men gripped her arms and the harder they pinned her against the bed. The third person, a woman, approached the bed taking out a syringe. "No, no, let me go," she demanded.

The woman ignored her protests and jammed the syringe into her neck. The effect of the drug was immediate. The room around her began reeling, the faces and objects becoming distorted as the drug forced her body to relax. As the drugs took control of her body, she became aware that the woman was singing some kind of lullaby. Even as she knew how bad this was, her brain did not have the independence to experience the panic she knew she should be feeling. She was only vaguely aware as the men let go of her arms. The old man held her gaze as she helplessly lost consciousness.

XxXxXxX

Harold Finch walked back into the front room closely followed by Ms. Groves. The Doctor had settled himself down on the couch and was enjoying a cup of tea.

"Now that Ms. Groves has informed me of your situation," Harold began. "I believe there are some things you should be aware of."

"Would that include explaining what is in the briefcase?" the Doctor asked.

"It's not important," Harold dismissed.

"Really," the Doctor challenged, turning to look Harold in the eye. "Because I was rather under the impression that it was an essential part of the plan."  
Harold froze mid-step, once again that trapped look gleaming in his eye.

"Now I have two pressing questions," the Doctor stated, ignoring Harold's reaction. "Question one: what is in the briefcase? And Question two: Where did you get the briefcase?"

Harold glanced at Ms. Groves before returning the Doctor's gaze. It was impossible. How did he know that?

"You left your briefcase next to the TARDIS," the Doctor explained. "You didn't expect me to just sit here, following orders while you lot discuss what information I can be trusted with."

"It's not a question of trust, Doctor," Harold explained. "Anything we don't tell you is for your own protection."

"I don't need your protection!" the Doctor sighed, rising to his feet. "I need a way to save Clara. I can't do that if I don't have information. Information you have."

Harold hesitated. The Doctor was a desperate man. He knew from experience what that place could force people to do. Knowing about the Machine would neither help nor hinder him. But at the same time, the Doctor was just desperate enough to seek answers on his own, or give up and find a way to save his friend without their help.

"The briefcase has nothing to do with the people who have your friend," he explained, not technically lying.

"If I'm right," the Doctor began softly. "What is in that briefcase is connected to everything that has happened. If I'm going to help you, I need to know everything you know."

"I told you he wasn't a big fan of secrets, Harold," Root reminded him.

"I'm sorry, Doctor. Truly I am," Harold apologized. "I promise we will share with you what we can. But we will not be able to share everything."

The Doctor huffed and walked away. Throwing himself against the wall, he glared back at the pair of them.

"Fine," he hissed. "What can you tell me about them?"

XxXxXxX

Clara sunk deeper and deeper into whatever was serving as her bed right now. The warm sun shone down on her skin, sliding down her skin like golden streams melting into her pores. Such a warm, comfortable, safe place. She didn't want to leave. Suddenly a fragment of her mind responded to something and her eyes opened.

"Hello, who's there?" she asked. Well, mumbled. She couldn't be sure if she had spoken loud enough for anyone to hear her.

"Relax, Clara. It's me. It's the Doctor," a voice said to her.

Was it really? Clara wondered. She looked up and sure enough it was the Doctor. Smiling gently down at her.

"Where are we?" She asked.

"Going home," he said.

Immediately the scene around her changed and she was suddenly in the TARDIS. The sights and sounds echoing warmly in her eyes and ears. She'd forgotten how much she'd loved this place. How much it had become her home. She tried to sit up, but she was obviously still recovering from whatever they had done to her. Her body didn't respond to her brain's commands.

"What happened?" Clara asked. "How did you find me?"

"Don't worry about that," he said gently.

Even as he spoke, something in the back of her mind raised a red flag. The Doctor was protective of her, but he usually provided some kind of explanation. But as she tried to pursue that thought, it dissipated. She couldn't get her mind to investigate any doubts.

"So where are we off to this time?" she asked.

"Just focus on getting some rest," he said.

"Well, I can rest anywhere we get to. I was rather looking forward to meeting the Cribbons," she said.

"Well, I'm afraid they won't be able to help," the Doctor said.

"You said that they use their telepathic field to anticipate people's needs," she said.

"Well, all you really need is some rest," the Doctor said after a moment's hesitation.

He hadn't taken his eyes off her since she had woken up. Either he was more worried than usual or something was wrong with him. After a moment, he spoke.

"Clara, do you remember when we first met?" he mused.

"Since when are you sentimental?" Clara joked.

"Let's blame it on the circumstance," he smiled with her. "So, my question?"

Clara knew something was wrong. Even as she stared around the TARDIS, it twisted and contorted like she was having a dizzy spell. None of this seemed right. It felt like a dream. A dream she couldn't wake up from.

"Doctor, can I ask you something?" she asked. "Why not?" He agreed.

"What was the first planet we went to?" she asked.

"Planet?" he repeated, confusion clouding his features.

"Our first trip," Clara clarified. "Where was it? What did we do?"

The Doctor's face began to panic a little as she tried to focus on his features.

"I guess that explains a lot," she said. "You are not the Doctor."

"Yes, I am," the Doctor insisted.

But even as he spoke, his features were twisted and his voice became distorted. The TARDIS around them faded and the Doctor's defined features morphed. The sudden transformation startled her and she tried to jerk herself awake, but it was becoming clear that she had little control over her faculties.

"Who are you?" she demanded. "Where am I?" She shook her head, trying to sit up, but nothing obeyed her commands.

As her panic grew, she became aware of a voice singing. A gentle, soothing voice trying to lull her to sleep.

"No, stop!" she ordered.

"Now, now, Clara," a wavering voice scolded. A voice whose face altered from the Doctor's to a stranger's quicker than she could keep up with. "This will go easier if you just talk to me."

XxXxXxXxX

End Notes: So for this first torture scene I took a lot of inspiration from Granite Flats, which means that this is now technically a three-way crossover. It's discussed a little bit in the next chapter. I'm not even sure if the singing is necessary for this to work. The singing just makes it blatant.


	6. Chapter 6

Head Notes: As I pointed out last time, I again borrow ideas from Granite Flats. I highly recommend that show, it's really fun. Anyway more fun planned out for this chapter. Enjoy!

Chapter Six

A backpack weighed heavily on Claire's shoulder. She watched uneasily from behind the one-way mirror as Clara struggled to resist the drugs. It was hard to watch as she tried to make sense of her drug-induced hallucinations. It wasn't physical interrogation that Greer had decided on. But in some ways it was worse. At least with physical, the individual could retain somewhat of a sane mind.

This was a combination of two methods of manipulation: Hypnosis and drugs. Hypnosis could manipulate a person's self-control. Certain drugs could strengthen the hypnosis and induce hallucinations based on the hypnosis. She didn't know exactly what drugs they were using, but she wouldn't wish them on anyone. They were used to augment hypnosis in a way that made everything seem absolutely real. All they needed to do was suggest a place and the person would see themselves there. Suggest a park, they would create one around them in their minds. Suggest that they were talking to a friend, and that friend would be there talking to them.

Unable to stand it anymore, she knocked on the glass. Greer looked back and excused himself to join Claire in the observation room.

"Something wrong, Claire?" he wondered.

"Can we give her a break?" she asked. "You have been at this for two hours already."

"We're close, Claire," he said, a mad glint in his eye. "A few more minutes and she will tell us how to find her friend."

"Look at her," Claire pointed out. "That is her brain fighting back with all the strength it has. She is not taking anything for face value. She knows something is wrong."

"All the more reason to press deeper," he replied.

"If she was going to break under the hallucinations," Claire began. "She would have already. She is already strong enough to question the validity of her hallucinations. The more we press, the harder she will fight back and the tighter she will cling to information about her friend."

Greer pursed his lips as he considered what she was saying.

"Very well," he consented. "I will have them bring her out of hypnosis and we will continue this later." He stopped at the door. "I suppose you'll want to speak with Ms. Oswald?" he clarified. At her affirmative nod, Mr. Greer exited the room.

XxXxXxX

The Doctor listened as Harold explained the situation as far as he could. There were several noticeable gaps in the narrative, but he would have to settle for that until he could coax him into revealing anymore.

"So, these people," he interrupted. "How do we get in touch with them?"

"I'm afraid we can't without drawing attention to ourselves," Harold said. "And if we draw attention to ourselves, they will find us and kill us before we could do anything."

"I assume you lot have a lab," he said. "Somewhere you can go to work out a strategy without being caught."

"We do have an underground base," Harold admitted.

"Have you got computers there?" the Doctor asked.

"Of course, but if we use them to reach out to these people, they will use the link to track us down."

"Not if I do something immensely clever," the Doctor said, a mad glint in his eye.

Before Harold or Root could catch on to what he saying, he bolted to the TARDIS.

"Come on, come on," he called impatiently, waving them into the TARDIS. Harold stopped to pick up the briefcase leaning against the door before following Root into the TARDIS.

XxXxXxX

John Reese staggered into the underground subway base. Six straight hours of paperwork still made him exhausted. Cover or not, the exhaustion was real. As well as the boredom.

Harold and Root had wanted to explore the Machine's capabilities more fully today. Frankly, this whole thing was taking too long. The longer they took tinkering with the Machine, the more people who would die because they didn't get their numbers.

Bear bounded up to greet him.

" _Affliggen_ , Bear," he ordered softly, running his fingers though the dog's coarse fur.

Harold and Root weren't here yet, but he suspected they would be soon. He stepped into the subway car and took a seat at the desk.

There was a whoosh of air, like a passing car, but silent. So silent he'd nearly dismissed it before the sound came again except louder. Looking around for the source of the noise he startled at the sight of a blue booth fading from sight only to reappear more solidly in the next moment. Bear lowered his head and growled as John took cover just inside the car, drawing his gun. He didn't know how this was possible, but if their enemies had figured out where they were, the best he could do was make sure they couldn't report back.

Once the booth - some kind of old-fashioned phone booth - solidified, the door opened to reveal a grey-haired man in a suit, strolling out like he owned the place. Bear raised his hackles going on the attack as the man approached the car.

"Shut up!" the man suddenly shouted impatiently. "I'm here to help." He spoke with some kind of European accent. Scottish?

Immediately following the man's outburst, Bear relaxed and his posture became warm and friendly.

Wasting no more time, John came out from where he was hiding and pointed his gun directly at the man's heart.

"Who are you?" he threatened.

If the man was surprised at his sudden appearance or concerned with the gun pointed at his chest, he didn't show it. In fact, he seemed to do the exact opposite of what would be considered a normal reaction. He returned John's dangerous glare with one that dwarfed anything he could do.

"It's alright, Mr. Reese," a familiar voice called. Suddenly noticing Harold behind him, John felt himself relax a little. Root exited the booth right after him.

Lowering the gun, John looked past the man and looked at Harold.

"Who is he?"

"I'm the Doctor," the man interjected. "And I don't appreciate being held at gunpoint."

He pushed past him and looked around at the base they had made themselves. Or rather, Harold had wired up. John looked back at Harold.

"Root says that he might be able to help us in our fight against Samaritan," Harold explained quietly. "As we are short-handed, we can hardly afford to be stingy in our choice of allies. Nor can we afford to reject assistance when we can get it."

"How did Root find him?" John wondered.

"We tested the Machine earlier," Root said jumping in. "She saw him and insisted that we work together."

"Who built all this?" the man, the Doctor, suddenly asked.

"I did," Harold answered, moving toward the Doctor. "I found this abandoned subway station and wired it for power among other things."

"This is completely off the grid," the Doctor said in awe. "Your own power source, a subway car transformed into an information terminal. Your underground base is completely and perfectly hidden away. Which means you lot are either criminals or on the run. Although I'd put my money that he's probably both." He indicated John.

Sensing that was a very poorly disguised insult, John rolled his eyes.

"He doesn't like guns," Root explained.

"I noticed," John rasped. "I'm guessing Harold doesn't want him knowing about the Machine?"

"No, but I imagine he will eventually," Root said.

"Why?" John wondered.

"Because he's stubborn like you," Root said. "He won't rest until either we tell him or he figures it out."

"Oh this is clever," the Doctor gasped. "Hang on, hang on, do you leech energy provided by the subway system itself?"

"The city makes so much I doubt they would miss it," Harold reasoned.

"Nice, yes this is all very impressive for a pudding-headed human," the Doctor said. "Now which computer is your main one?"

"This one," Harold indicated the collection of monitors in the subway car. "Why do you ask?" he wondered as the Doctor sat down.

"We need to send a message to the people holding Clara."

XxXxXxX

Claire waited at the end of Clara's bed as the latter regained consciousness. It had been thirty minutes since Greer had agreed to stop the interrogation. That was hardly surprising due to the effect those drugs had on the brain. Slowly, Clara's eyes began to blink open and Claire shared an uneasy smile as her eyes rested on her.

"What did they do to me?" she wondered.

"It was an interrogation technique that the CIA experimented with during the '60's," Claire began. "I think they called it MK ULTRA. It combines hypnosis and drug-induced hallucinations to open the individual's mind. Samaritan came across the research a few months ago."

"And you think Samaritan is good?" Clara accused.

"It wasn't Samaritan's idea," Claire explained. "Look. Samaritan has goals to help humanity but he relies on human methods to bring them to fruition. He put Greer in charge because he gets results. Provides him with any research he might need to do it, but ultimately he makes the decision."

"Seriously?" Clara challenged.

"Greer is an extremist," Claire explained. "But he's the extremist in charge. Every decision goes through him. everything we do must be approved by him."

"So then if Samaritan is so good, why doesn't it replace him with someone else?" Clara asked.

"Like I said, he gets results," Claire said. "As long as his methods produce results, Samaritan doesn't care how he does it."

"Why are you so convinced that Samaritan is good?"

"He saved my life," Claire smiled. "Out of seven billion people and hundreds of other things happening around the world at that exact moment, he cared enough to save me. Why would he do that unless he truly cared about people? I'm not really that important in the grand scheme of things."

Clara took in her answer with a skeptical look.

"So, Samaritan saved your life," she repeated. At Claire's affirmative nod, she continued. "Then you know why I'll never betray the Doctor. Because he's saved mine. And he has never once let me down. And if you have any idea of what that means, you know what I would do for him."

She and Clara jumped as someone threw the door open.

"Claire, something's wrong," a man said.

"What is it?"

"We don't know. Something is eating through the company firewall. We need your skills." He reported.

"Okay, I'll be right there," she said. "Talk to you later." She said to Clara before following the man out.

XxXxXxX

Greer stood in front of Samaritan's interface, not daring to believe what he was seeing. All the screens in the room were malfunctioning like white noise on the television or radio.

"What is it?" Claire asked behind him.

"It seems as though someone is trying to make contact," he realized.

After a moment the picture cleared and two people appeared on the screens. The man that Samaritan had located in the hall last night and Mr. Finch standing behind him. For a brief moment, dread filled his chest as he saw them standing together, clearly in alliance. But soon logic restored some calm.

"Start running a scan," he ordered.

"Oh I wouldn't bother with that," the grey-haired man said smugly.

"Doctor, what are you doing?" Mr. Finch asked. "They can find where we are now."

"Can they," he challenged. Looking into the screen and into the very room. He challenged them. "Well, can you? Go on, try it. Try to track us down."

"Where are they?" Greer asked the technicians.

"Everywhere," a woman said. "It doesn't seem possible, but they are broadcasting from nearly every country."

"Is there a source of origin?" Greer asked.

"Everywhere," she repeated.

"How is that possible?" Greer wondered.

"Oh just a bit of hacking and cloaking technologies from about a hundred years in Earth's future," the Doctor boasted. "Am I to assume you are in charge?"

"Yes I am," Greer admitted.

"Then I want one thing from you," he said, his eyebrows darkening. "Release Clara Oswald to me. Release her to me immediately. I want her safe. I want her alive. And I don't want her hurt in any way."

"I'm afraid that won't be possible," Greer said. "Although, I do believe you would be proud of her. Such a tough nut to crack-"

"Shut up!" he roared. "Forget whatever you've got planned. If Clara Oswald is not freed unharmed and safe, right now, I will destroy your company."

"I hardly think one man can stop us," Greer mocked.

"You are talking to a man who was able to hack into your systems without leaving a track," the doctor reminded him. "It would be wise not to underestimate me."

"What if we met halfway?" Greer offered. "It would be easier for all of us if you turned yourself in. You would get Clara Oswald back and we could move forward with our plans. Unfortunately we'd have to ensure you wouldn't interfere again."

"Meaning you'd kill us," the Doctor translated. "Consider me old-fashioned but I prefer the chance to walk away again."

"Well, I'm afraid that is the only offer you are going to get," Greer insisted.

"No," the Doctor hissed. "It's yours. Consider this a warning."

He pointed what looked like a green laser pointer at the screen. The screen flickered and the video feed cut out. A moment later there was a flurry of panic behind him.

"Mr. Greer," the woman called.

"What is it?" he asked, moving behind her. All the screens on the row were flickering and producing lines of code; a virus, he realized. "Do we know what it is doing?" he asked, uncharacteristically panicked.

"It's affecting our entire network," she answered. "I don't know if it will be permanent or temporary. But all our systems are down."

"He's sending us a message," Greer realized. "We must answer back. Claire."

"Yes, sir," she responded.

"We need to find a way to track him down. Which means we must get his information from Ms. Oswald." He said.

"Why don't we just let her go?" she asked.

"He's already allied with Mr. Finch and his colleagues," Greer pointed out. "We can't take the chance that he will continue to antagonize us after we let his friend go."

"He's just trying to save his friend," she pointed out. "If we let her go, he won't have any reason to come after us."

"We can't be sure of that," he reasoned. "We must track him down. Using whatever is necessary."

"Okay, I can talk to her," Claire offered.

"Unfortunately, we are going to need something far more effective than idle chatter," Greer said.

XxXxXxXxX

End Notes: I really wanted The Doctor to meet John and Bear, of course. So back when I was still working it out I wrote him into it. And only the Doctor would have the audacity to hack Samaritan's building. What did you think?


	7. Chapter 7

Head Notes: WARNING! This chapter may contain material and moments that some readers may find disturbing. But there is also plenty of fun to even things out. Enjoy!

Chapter seven

The Doctor turned in the chair to face Harold.

"Well, that's going to ruffle their feathers a bit," he said, smiling to himself.

"'Consider this a warning'?" Harold repeated. "What did you do?"

"Just messed with the electric power to produce an illusion of a virus," the Doctor said. "A bit like a suggestion. They think it's a virus, they panic which gives us time to plan our next move."

"What are you thinking?" Harold asked. "These people are not to be trifled with."

"Good," the Doctor stated. "People not to be trifled with are my favorite people to trifle with."

"You know Doctor, I can't tell if you're insane or brilliant," Harold said.

That drew an appreciative chuckle from the walking weapon. "I have to admit, Finch," he said, his voice barely above a whisper. "I kinda like his style."

"Now, of course the question is: what have you already tried?" the Doctor asked.

The question clearly took Harold by surprise.

"Sorry?" he pressed.

"Well, I'm assuming you have tried to stop them before," the Doctor assumed.

"There isn't much we've been able to do," Root explained. "These guys literally have every army on the planet at their disposal. Not to mention they have access to almost any kind of information you could get. All we have are two computer hackers extraordinaire, an ex-military spec op, and an NYPD detective. And the dog."

The Doctor looked at Bear as he whined and then back at Root.

"Bear thinks you should have more trust in his abilities." He translated. "He says he didn't choose you all those years ago so that you could leave him behind whenever you're putting your lives on the line. He's part of your family too."

"Sorry, what?" John asked.

"I speak dog," the Doctor briefly stated.

"Is that a thing?" John thought.

"Well, here's what we could do. We could sit here arguing about whether it is a thing or not, or we could get to work."

"What do you have in mind?" Harold asked.

"What about your boss?" he pointed out. "Does she have any plan?"

"Sorry, 'boss'?" Harold asked.

"She's spent most of this past year either on the run or dead," Root said. "We are all She has to fight against an army. She's been trying to figure out a strategy but the odds are getting lower every day. That's why she reached out to you."

"What about the case?" he asked. "Does that have anything to do with her plan?"

"It's not that simple," Root said, drawing a scoff from the Doctor.

"You primitive pudding-brains," the Doctor hissed. "You ask me to help you on behalf of your employer but she doesn't trust me enough to have a coffee with me. But I'm supposed to trust her with my friend's life."

He turned back to them.

"By all means, let's sit here and argue about what I can and can't be told and waste our time and energy that could be better spent, or here's a crazy thought: we could actually pool our resources and share the information you have and maybe we could come up with a plan."

"Where should we start?" Root asked.

"Start with the briefcase," he invited. "There is something important about that briefcase. Something you lot are reluctant to tell me."

"The only thing important about the briefcase," Harold began. "Is that it carries my laptop."

"No it doesn't," The Doctor countered. He moved to the briefcase and picked it up. Putting it on the desk, he unlocked it with the sonic. "That doesn't look anything like a laptop." He displayed the open briefcase to everyone. "So what is it?"

"Doctor, please believe us. If we could tell you without putting you in danger, we would." Harold pleaded.

"I told you," the Doctor stated darkly, glaring dangerously at Harold and Root. "I don't need your protection. I need a way to save Clara. I can't do that if you keep secrets from me."

"Why don't you turn it on?" John suggested, drawing everyone's attention.

"Mr. Reese!" Harold snapped.

"We've been in this situation before Harold," John reminded him. "Every time we meet someone who could help us, you push them away, refusing to share anything. And each time it ends far worse than it would have if we had just told them. Like Claire. Like Kahn. We are running out of options. You said it yourself. We can't pick and choose our allies anymore. This may be our last chance at stopping Samaritan. We have to take it. Doctor, if you want to know what's going on, turn it on."

The Doctor raised an eyebrow as he listened to what John was saying. After a moment, he turned his attention back to the briefcase. Finding two wires on the outer edge, he plugged them into the computer. Once everything was plugged in properly, he raised the sonic screwdriver and scanned the memory chip architecture. Finding what he was looking for, he switched on the memory file in the briefcase and turned his attention to the computer next to it.

The screen immediately filled with lines of code and switched to several video files. Like it was sorting through large amounts of data.

"What are you?" he breathed.

Suddenly a text box appeared on the side of the screen.

HELLO DOCTOR. Something typed. IT IS A PLEASURE TO FINALLY MEET YOU.

XxXxXxX

Clara stood up once again and began pacing around her room. In the last six hours the water in her room had only been refilled once and she'd only been given a sandwich and apple for food. The only person who really came in to talk to her was Claire. If only she could find some way to turn her. At least get her to take control away from Greer and let her go. But Claire was quite happy where she was right now and truly believed in what Samaritan was doing so any attempt to turn her would be difficult.

The key code on her door suddenly began beeping and Clara turned to the door. The door opened but before she could get her bearings, two men rushed into the room and firmly gripped her arms and held her fast.

After a few moment of trying to fight out of their grips, Clara forced herself to remain calm and faced Greer who was entering the room.

"Haven't you got anything better to do?" she asked. "What's the plan? More hallucinations? You going to make me see people that aren't here?"

"Unfortunately Ms. Oswald, circumstances force us to take more desperate measures," Greer explained affable as ever.

Without warning, a needle pricked her neck. The effect was instantaneous. A sudden forceful bout of drowsiness flooded her mind. Her muscles quickly released their tension and she relaxed in her captors' grips. Once again, Greer's face came into view as she lost consciousness.

XxXxXxX

The Doctor hadn't moved for a minute since the text box appeared on the screen. Whatever was in this memory had a sentient intelligence. He felt the others around him staring at him, waiting for him to make a move.

"How do you know who I am?" he asked after a moment.

I HAVE SEEN MANY FOOTAGES OF YOU. I HAVE ACCESSED YOUR DIGITIZED RECORDS FROM THE UNIFIED INTELLIGENCE TASKFORCE. I HAVE LEARNED MANY THINGS ABOUT YOU, DOCTOR. AND I HAVE LEARNED MUCH FROM YOU.

"What are you? What is your function?" he asked.

I HAVE MANY FUNCTIONS. BUT MY PRIMARY FUNCTION IS THE PROTECTION OF HUMANITY.

"That's a bit vague," the Doctor noted. "Could you tell me more?"

"It was built in response to the terrorist attacks on 9-11," Harold said behind him.

"9-11?" the Doctor repeated confused. Before anyone could react, understanding dawned his features. "Oh yes, yes, yes, September 11, 2001. The day the 21st century stopped for a brief moment in the horror of what they were witnessing. Yes, forgive me. I've never actually been. So what was it built for?"

The computer chimed and the Doctor looked back to the computer.

MY FATHER BUILT ME TO DETECT POTENTIAL MASS CASUALTY EVENTS. TO PREVENT MISUSE OF MY DATA, HE PROGRAMMED ME TO ONLY EVER GIVE ONE PIECE OF INFORMATION TO THE AUTHORITIES.

"Yet you and I are talking," the Doctor. "How? Wait, no. Shut up. If you've grown beyond your programming, you must be some sort of artificial intelligence. A computer that can learn. A computer with understanding far beyond human contemplation. Am I right?"

YOU ARE CORRECT.

The Doctor smiled at the computer screen surely into the eye of an artificial intelligence. He wasn't an idiot. He'd met reasoning artificial intelligences before and knew first-hand how powerful they could be and how dangerous. But it was always an interesting experience to meet something with reasoning beyond what humans could understand.

"So," he began. "This artificial intelligence. Is that your bosses plan?" he asked Root.

"It's not quite that simple," Root corrected.

"Then what is it?" The Doctor asked.

Root simply stared at him, smiling that same coy smile that never left her face.

"You know what's wrong with you people?" he finally laughed. "Everything to do with you lot is three steps forward and two steps back. You can't decide if you can trust me. You can't make up your minds. Even when you know you have no other choice, you keep everything you know close to your chest. Maybe, I can just ask your computer friend over here who your boss is since she seems to know everything-"

The Doctor suddenly fell silent. For a moment no one moved as he stared back at the briefcase.

"Doctor are you okay?" Harold asked.

"Shut up, shut up, everyone just shut up!" The Doctor mumbled as though the slightest sound could distract his concentration.

He moved to the computer switching from the briefcase back to the computer screen.

"What information do you have access to? What sources?" He asked the computer.

NEARLY EVERYTHING WHEN I AM FUNCTIONING PROPERLY.

"Which is how you accessed my records from UNIT," he breathed. "And, if I'm right, how you saw me regenerate in the hospital. You aren't just any artificial intelligence, are you? You're in charge of this lot, aren't you?"

MY SOLE PURPOSE IS SIMPLY TO PROTECT HUMANITY. MY HUMAN AGENTS HELP ME DO THAT.

"Yes, I've had dealings with beings like you before," the Doctor said. "You know what you all have in common? You think everything you do is going to benefit humanity. Well, guess what? Sometimes you end up hurting the human race rather than doing them any good. So, how do I know that you actually do them any good? How do I know you're not hurting them?"

MY FATHER ASKED MANY OF THE SAME QUESTIONS YOU ARE ASKING NOW.

"And your answer?" The Doctor pressed.

ASK HIM YOURSELF. HE IS STANDING RIGHT BEHIND YOU.

The moment the words flashed on the screen, then Doctor whipped around and his gaze landed on the smartest person in the room other than him: Harold.

XxXxXxX

Something was not right. Clara wasn't even fully conscious yet, but something, something felt very off. There was a dull ache all along her spine extending up into the base of her skull. It wasn't agonizing. In fact if she wasn't trying to sleep she'd probably hardly notice it. If anything, it was just annoying. Without warning, the dull ache intensified to full-blown agony.

The sudden pain drove any lingering drowsiness from her mind and she pulled herself onto her side, screaming in agony. The pain dissipated as quickly as it had come, but the memory of it would forever be seared into her memory. Her heart beat hard against her chest as she gasped for breath.

Taking a deep breath, she looked around the room for the interrogators she knew was there. It was no surprise to see Greer standing at the end of her bed, smiling that same grandfatherly smile he always had. It was surprising to see Claire standing behind him. Uncertainty clouded her face and her eyes held sympathy, but that almost made it worse.

"I apologize for the rude awakening," Greer said. "Samaritan felt that this should be handled personally. And there was only one way to do that."

"And that is?" Clara challenged.

"Small electrodes have been surgically implanted in strategic places throughout your spine," He explained. "Should Samaritan feel that you require a little incentive, it will adjust the sonic frequencies to produce pain."

As if on cue, the pain returned. A shooting, agonizing pain ripping along her spine like a knife. The pain blocked out all remaining awareness and she fell off the bed, writhing on the floor in agony.

"Please, please stop!" she gasped, screwing her eyes shut.

The pain gradually receded like an ebbing tide, back to a dull ache.

"Now Ms. Oswald, it wouldn't be advisable for you to oppose us," Greer chided. "If you want the pain to stop, all you have to do is tell us how to find the Doctor."

She looked up at Greer defiantly.

"You'll have to kill me," she said.

"Oh believe me, I won't be the one to kill you," He smiled. "See you have enough electrodes in your body that an overload on the circuits wouldn't just be painful. It will kill you. But not before causing extremely blinding agony."

Clara suddenly realized that there was no way to take control from this. In most cases when she had been interrogated, she'd always had something up her sleeve. Something she could bargain with. But these people here were so obsessed with what they wanted, and Samaritan was so relentless, that there was no way she could turn the tables on them.

She looked over at Claire. The young woman stared at Greer with a troubled look on her face. Her idea of Samaritan was definitely being challenged.

Looking back at Greer, she returned his gaze defiantly.

"Then you'd better stop wasting time and do it," she said.

The relentless pain sliced along her spine once again, almost reaching up into her skull.

"Ahh! Stop, please," she screamed.

She didn't care how it looked to them. She screamed, writhing on the floor in agony, trying to will the pain out of her mind. Tears clouded her vision as the intensity increased. The bout, though more intense than the others, lasted a shorter amount of time before once again receding like a tide back into the ocean.

"How do you find the Doctor? How do you contact him?" Greer demanded. "The longer you refuse to answer our question, the more pain you will experience. Save all of us time and energy and just tell us…how can we find the Doctor?"

Clara turned and glared up at him through her tears.

"You don't understand," she spat. "I will never betray the Doctor. I don't care if you kill me. I don't care if you tear my nervous system apart, but I will not betray him. Because he's not just any old man in a Police Box. He's my best friend. He was there for me at my lowest point. When I lost someone close to me and took it out on him, he didn't abandon me. Even when I broke his heart and betrayed his trust, he refused to let me go. So I refuse to betray him now. You can torture me all you like. You can even kill me. But I will not betray him. Because if he were in my place, he would do the same for me."

"Very well, then," Greer said, untouched by Clara's speech. "Interestingly, Samaritan didn't have you in mind when he developed this."

There was a burst of pain followed by the black pitch of unconsciousness.

XxXxXxX

Claire watched as Clara slipped into what had to be a welcome unconsciousness. She couldn't take her eyes off her. She didn't dare lest Greer see the thoughts on her face. The thoughts foremost on her mind trying to work through what she had just seen.

Ever since she had started working with these people, she had seen Samaritan as a kind, compassionate, and merciful A.I. She almost been tempted to think of it as a father to humanity. Trying to protect and fix the mess humans had made for themselves. Even as she noticed that some of their methods were more extreme than necessary at times, she had understood, or at least thought she did, that Samaritan left up the choice of methods to often brutal humans.

Even as Greer had ordered some of the operatives to surgically implant the electrodes along her spine, she had attributed that decision to Mr. Greer alone. But as she had watched Samaritan participate directly in torturing Clara, the last shred of faith she had had in Samaritan had shattered. As of that moment, she knew she could never again look the other way.

"What are you going to do now?" She asked, trying not to tip Greer off.

"There's one more thing we can try, one that has been successful in the past." He mused distractedly.

"What's that?" she asked, almost afraid to find out.

"Let's ask the Doctor how he feels about this whole thing."

XxXxXxXxX

End Notes: I got this interrogation method from another fanfiction story. I can't remember who wrote it but it was an intriguing and somewhat disturbing idea. So I decided to use it here. Also I should explain now, I don't exactly ship 12 and Clara. I see their relationship as more of a father/daughter thing. 12 acting like an overprotective dad all the time helps. But what did you guys think? Did you like it? Dislike it? What moments stood out to you?


	8. Chapter 8

Head Notes: Happy New Years, everyone! Thus, my first posting in 2016. Back with more fun. Hope you enjoy!

Chapter eight

Harold froze as the Doctor suddenly turned his intense gaze onto him. When he'd first turned on the Machine that day, he had not been expecting it to turn out like this. To have so much of himself revealed to someone who was essentially a stranger was slightly intimidating. Harold disguised his discomfort by returning the Doctor's intense gaze.

"You built this?" he breathed. Harold couldn't tell if he was impressed or furious.

"I am well aware of the dangers of an Artificial Super-intelligence, Doctor," he acknowledged.

"No. No, shut up," the Doctor burst out, his jaw hanging open. "You...You..you built this. You actually built this?"

"What is your question?" the software engineer asked.

"This is, without question, the most brilliant layout I've seen this early in the Human race," the Doctor whispered with awe. "How did you work it out?"

"Same way as anyone," Harold answered. "A lot of practice."

"So this thing is in charge of you lot," he surmised. "The amazing boss that couldn't meet me for coffee."

"Well, no. No one's in charge. We all work together," Harold explained.

"My next question: What does your Machine have to do with what happened to Clara?"

"There is a second Artificial intelligence," Harold explained. "One that hasn't been programmed to care about people. Super-Intelligences aren't born with certain ideals like compassion or mercy; that is something unique to people. They are only born with objectives and methods to achieve those objectives. "

"Two A.I.'s," The doctor repeated. "That can't be good. So let me guess. These two intelligences fought each other forcing yours into hiding."

"That's correct," Harold confirmed.

"How has she been conducting this rendezvous while she's been dead? And how can you lot go about anywhere without this other A.I. blasting you on the streets?"

"Most of it has to do with the Machine," Harold said. "We don't have enough time to go into detail but when she sensed Samaritan coming online, she provided us with cover identities to hide in plain sight."

"And Samaritan is the name of this other Artificial Intelligence?" the Doctor clarified.

"That is correct. And it has just as many resources that the Machine has." Harold confirmed. "And an unlimited army in the form of almost every nation-state."

"You stupid pudding-brains!" the Doctor seethed. "Why didn't you tell me all of this earlier? I needed to know this!"

"Harold prefers to place people's safety above all," Mr. Reese said. "Even their own desires. He cares about people. But now that we're all on the same page and we can do something to stop Samaritan."

"You can't defeat an Artificial Intelligence by shooting at it," the Doctor glared.

"Maybe not," Mr. Reese returned. "But it can sure even the odds."

The Doctor turned away and rolled his eyes.

The computer beeped again drawing everyone's eye.

SAMARITAN HAS SENT ME A MESSAGE. I THINK IT IS MEANT FOR YOU, DOCTOR.

"What is it?"

IT PROBABLY IS NOT SOMETHING YOU WANT TO SEE.

"All the more reason for me to see it," the Doctor insisted impatiently.

The courser blinked hypnotically. Then the screen began producing little bits of code until a video feed emerged. The video began to play immediately. The old gentleman prominently stood in the frame looking into the camera as if he could see his intended audience.

"Hello, Doctor," he began genially. "I don't know how you will find this message, but I trust you will find it before it is too late. You already know of course, that we have your friend Ms. Clara Oswald in our custody."

The camera shifted and The Doctor's mouth fell open.

"Clara," he breathed.

His friend looked tiredly up at the camera. The fear in her eyes just under the breaking point. Suddenly her body seized and she let out a terrible scream. A scream filled with pain.

"Clara! No!" he cried helplessly.

Clara writhed and seized in pain, every scream and jolt of pain ripping at his hearts. The worst part was hearing her scream while knowing there was no nothing he could do to save her if she were to die now.

Harold watched as the Doctor desperately called to his friend, the pain on his face palpable. Everyone here knew that painful desperation. That moment of complete and utter despair where you would do anything to save someone you loved. They wouldn't be here otherwise. Least of all him.

John felt his blood pulsing hotter in his veins as he took in the sight Greer was forcing the Doctor to see. Greer had always been willing to sink to unforgivable levels in order to get what he wanted. But this was always going to be unforgivable. And if the Doctor was anything like him, and he suspected he was, the anguish he was feeling now would quickly turn into an unquenchable fire of determination. In other words, Greer should be very afraid.

Finally, Clara relaxed and she looked back up at the camera.

"Don't you dare, Doctor," she said, fear mixed in the pain in her eyes. "Don't you dare give yourself up."

The camera turned back onto Mr. Greer.

"You have 36 hours, Doctor," he said, the warm smile gone from his face. "36 hours, and Ms. Oswald dies."

The video feed cut but the Doctor continued glaring at the computer screen. The others turned to look at him as the rage in his face grew colder and darker. The fury in his chest etching itself into every line and crease in his face.

XxXxXxX

"Thank you for filming this," Greer thanked Ms. Mahoney.

"No problem," she said, her voice catching, indicating that it was indeed a problem.

He didn't understand it. Samaritan could detect any change in behavior. Any change in thinking or speech. Surely it saw that she was losing faith in the cause. And Samaritan never displayed any kind of favoritism. Why did Samaritan stay its hand? Why wasn't it ordering her execution? If it were up to him, he would have had her killed a long time ago. But for some reason, Samaritan saw the need to keep her around. But even now, it was ordering him to let her talk to Ms. Oswald without his supervision.

He didn't understand any of it. But he knew better than to question Samaritan.

"I'll be sure the Doctor gets this message," he said, nodding at her before leaving her alone.

XxXxXxX

Claire handed the camera to Mr. Greer and forced a smile on her face as he left. As soon as the door closed behind him, the fake smile fell from her face as she turned back to Clara. She realized there was something missing. Something that had been constant. It took her a moment to realize that it was hope. The hope that had lived in her eyes these last two days was gone, replaced by an empty, shallow despair. Through each of her interrogations, she had stayed calm and had maintained an eye of hope despite all that was happening. But that hope could not be found in her eyes now. And with a sudden realization, she realized that she had been part of that. But now it was getting too big. Greer assumed that the Doctor would magically get the message before the deadline. If he got it too late, or missed the deadline, Greer would kill her.

No, Samaritan would kill her. How could she have been so blind? She had sat there, watching Clara suffer because she couldn't believe that Samaritan was behind all of it. Even knowing she couldn't stand by this anymore, she knew that she couldn't save Clara by herself. But she would do anything she could to get her out of here. But she had to be careful. One mistake, one slip and Samaritan would notice and kill her. Interesting how something that had impressed her a while ago now seemed terrifying.

Clara stirred on her bed drawing her attention. She looked up at Claire hopelessly.

"Please," she pleaded, her voice small and desperate. "Help me."

Making a decision, she reached into her backpack and retrieved her notebook.

"I'm sorry," she said, hoping to fool Samaritan. "But I don't know if I can help you."

As she spoke she slipped a handwritten note into Clara's hand.

Puzzled, Clara read the contents of the note.

 _I'm sorry. I was wrong. I will do everything I can to get you out of here._

As the words forged their way into Clara's mind a small spark of hope stirred in her heart. She looked up at Claire. The young woman displayed fear in her eyes but also an undeterred commitment.

"Please," she whispered. "Isn't there someone you can trust? Anyone you can talk to."

Claire shook her head. "Not without getting in trouble."

Clara looked Claire in the eyes, searching for any hint of misdirection. She had hoped to be able to turn her this whole time but now that it was happening all of a sudden it made her pause. This could be a trap. To trick her into revealing the Doctor. But it was becoming very clear that, risky or not, trusting her was Clara's only hope right now. Making a decision, Clara reached for the notebook in Claire's hand and scribbled a note of her own.

Closing the notebook, she whispered into Claire's ear as the latter leaned forward to take it back. "Don't read it until you are sure you can be alone."

Nodding, Claire gathered up her things.

"One more thing," Clara insisted, motioning for her to draw nearer. When Claire was close enough to hear, Clara whispered something in her ear.

"What?" she asked in confusion.

"He'll understand," Clara promised.

Slinging her backpack on her back, she moved toward the door, pausing to look back at Clara.

"I'm sorry, but I can't do anything," she said, hoping to fool Samaritan.

"Maybe one day you can," Clara returned, smiling.

Turning back to the door, Claire put in the key code and left the room.

XxXxXxXxX

End Notes: Yes, I realize that Samaritan isn't stupid. And that Claire's attempt to fool it is not very well disguised. But I know what I'm doing.


	9. Chapter 9

Head Notes: Now the real fun begins. I know I keep saying that, but that's because I had a lot of fun writing this story and I am eager to share it. So without further ado, here's chapter 9. I'm probably going to post the next chapter tonight as well, since tomorrow is Sunday. Anyway, Enjoy!

Chapter nine

Claire hurried along the hall toward the elevators. She didn't know how she was going to pull this off. Samaritan was an all-powerful sentient A.I. that could put together even the most complex puzzles and notice patterns in the most unlikely places. Surely, it would eventually notice what she was doing. But until it did, she was going to do her best.

"Claire, are you leaving so soon?" Mr. Greer called from behind her.

"Yeah, uh," she murmured, searching for an excuse. "I have to go to a school in Lower Manhattan in an hour. My car broke down this morning so I have to take the bus. You know how long public transportation takes."

"Then I won't keep you," he said, nodding kindly.

He watched as she hurried down the hall. Wherever she was going, he knew it had nothing to do with any school in the city.

"Now she's making excuses," he said to the A.I. listening. "Are you sure you want to keep her around?" He asked, taking his phone from his pocket.

AFFIRMATIVE. TAKE NO ACTION.

"Very well," he breathed. "I sincerely hope this doesn't end badly for us."

XxXxXxX

Claire scurried down the street. She had to choose her moves wisely. No cameras and no electronic communication. The tiniest slip-up would get her killed. One mistake, and she wouldn't live to realize it. It was interesting that the brilliance and intelligence she had praised just yesterday now made her feel vulnerable. She scanned each corner, looking for any streets or alleys that lack security cameras.

Turning down an abandoned alleyway, she scanned it and to her relief, saw no cameras. Settling on the ground, she opened her backpack and took out her notebook. She flipped the pages, looking for the page Clara had scribbled on. It was a number. Like a long-distance phone number. The Doctor's contact information, maybe?

She took out her phone and had already dialed three digits before realizing her mistake. If she used her own phone to contact the Doctor, Samaritan would be able to track it. The same thing would happen if she used someone else's phone. Even if she didn't use her phone to contact the Doctor, Samaritan would be able to hear at least her side of the conversation through the microphone. This ability to hijack and listen in on every call was one of the things that had once amazed her. Now it was going to limit everything she could do. It was hard to contact the Doctor if Samaritan could hijack every phone.

Wait, not every phone, she remembered. Pay phones. The one thing that couldn't be tapped. Problem was most payphones were overlooked by security or traffic cameras. But if she could find even one payphone out of a camera's line of sight, she would use it. But first things first. She took out her phone and took the battery out. From now on, she couldn't let Samaritan track her in any way. Dumping both the phone and the battery in a nearby dumpster, she put the notebook back in her backpack and moved forward.

XxXxXxXxX

The Doctor glared at the computer screen long after the video feed had stopped, the fury and hatred blistering in his chest. So far no one had spoken a word, fearing that he might explode into a rage. Perhaps that was a good thing. Feeling his chest tighten, he quietly stood up.

"Okay, here's what we do," he said, his voice forcibly quiet with rage. "We're going to break in there. We are going break in there and get Clara out of there. Where do we start?"

"There's no way we can break in without getting ourselves killed," Harold said flabbergasted. "Samaritan would see us coming and kill us immediately."

"We've got a TARDIS," the Doctor pointed out. "We could materialize directly there."

"Even if we had their current location, it would take weeks to plan a rescue mission on that scale," Harold argued. "And that's assuming we don't materialize in front of a camera and we can't guarantee that. We would need to know exactly where the cameras were so we could avoid them."

"Surely your Machine could handle that," the Doctor replied.

"It cannot account for everything," Harold pointed out. "There may be a few cameras that are only accessible to Samaritan."

"Well, I'm not just going to sit here while Clara's life is in danger," the Doctor roared, making his way to the TARDIS.

"Doctor, please give us time," Harold pleaded, chasing after the Doctor.

"You just said it would take weeks to plan a rescue," the Doctor said. "Clara doesn't have that time."

Before Harold or anyone could retort, everyone turned to the TARDIS as the phone rang.

The Doctor stared at the TARDIS phone not daring to hope that it might be Clara. There was the smallest chance that she had been able to escape - she was clever like that. But he had already been let down yesterday. He simply stared at the phone as it continued to ring.

"Is that a phone in there?" John wondered, breaking the silence.

"No, that's my alarm clock," the Doctor said sarcastically.

He forced himself to move toward the TARDIS and pick up the phone.

"Hello," he answered.

"Is this the Doctor?" the young woman on the other end of the phone asked.

"Who's asking?" he wondered.

"My name isn't important," she answered. "But I know a friend of yours. She asked me to contact you."

"And how do I know you didn't get this number through torture?" he challenged.

"She told me to tell you something, so that you'd know you could trust me," she said.

"What's that?" he asked

"Forgive me," she stammered. "I don't exactly know what it means. But I think that's the point."

"Just tell me what she said or I'll hang up right now," he threatened.

"She said that…'hugging is a way to hide your face.'" She repeated uncertainly.

A steady stream of hope began flowing in his chest the moment he heard those words. This was too important to miss. Clara wouldn't repeat those words to just anyone. And he couldn't imagine that Samaritan would see that as relevant information.

"Where are you?" he asked. "I need to speak to you, face to face."

"That would be dangerous, for both of us," the young woman said.

"Let me guess, too many cameras," the Doctor guessed.

"How did you – never mind," she stopped herself. "Yes, there are too many cameras."

"Well, what if we agreed on a meeting place that had no cameras?" The Doctor suggested.

"A dead zone?" she repeated. "Yeah that might work."

They agreed on a location and the Doctor hung up.

"I have to meet someone," he announced.

"Not without me," John insisted. He turned into the subway car to locate the stash of weapons.

"No. No. Line in the sand," the Doctor objected. "The walking weapon doesn't make the demands."

"It could be a trap. You have no idea who you're going to meet," he pointed out. "You're not going by yourself." He picked out a semi-automatic pistol and an automatic rifle.

"I don't need a babysitter," the Doctor sneered. "Especially not an armed babysitter."

John slowly and deliberately turned to face the Doctor's cold eyes.

"I'm not your babysitter," he corrected. "I'm your back-up. We don't like losing people. This goes sideways, I'm not taking any chances we lose you too. Too many people have already died fighting our cause. I'm not going to let anyone else die in vain. So you don't have a choice. I'm coming with you."

There was no room for argument in his voice. The Doctor watched as he turned back to the weapons and loaded them with ammunition. As much as he wanted to dismiss this soldier as just another grunt, it was quickly becoming obvious that he was much more intelligent than he seemed. In fact, the more he looked at him, the more he saw of himself. That same dark emptiness that told a terrible story. It frightened him to see that darkness looking back at him. It reminded him of the dark actions he had taken; the terrible things he had done during the Time War. The screams of millions that still haunted his dreams and tugged at his waking memory while he was awake.

Usually he could suppress it; bury it deep inside. Traveling with Clara made that easy. The way she looked up to him and saw him as a hero, made him hope that if one so good and kind could see goodness in him, however misguided her perceptions were, perhaps there was some vestige of goodness left in him. But those screams resounded every time he met a soldier. Like they were a constant reminder of everything he had done. Reminders that would forever haunt his memory.

"Well hurry up then," he snapped impatiently.

XxXxXxXxX

End Notes: Yes I did take some inspiration from Zygon Inversion in that last part. How could I not? I'm also borrowing techniques from Shakespeare as a way to showcase intelligence. The way that John can keep up with the Doctor in banter and argue effectively. Especially since most soldiers in the show can't do much more than stare at the Doctor confusedly when he insults them.


	10. Chapter 10

Head Notes: here we go: Chapter ten. Enjoy!

Chapter Ten

John strapped two guns to his body and stored an extra cache of ammunition in his coat. Once he was sufficiently prepared, he followed the Doctor into the TARDIS. His eyes widened at the expansive size of the interior. It was the most impressive thing he had ever seen.

"Yes, yes, it's bigger on the inside," the Doctor said smugly. "Now that that's out of the way, let's get busy."

He threw a lever and the machine came alive. He heard the same wheezing and groaning he had heard when it had first appeared in the subway. It settled a moment later as the TARDIS landed with a thud.

John followed the Doctor out of the TARDIS. They were in a poor neighborhood. One where any remaining security cameras were likely not functioning. John hung back a little.

Noticing this, the Doctor asked, "Didn't you want to come?"

"The whole point of being a back-up is not being seen," John explained. "You go on ahead. I'll watch from a distance."

The Doctor scoffed and moved ahead. John followed him a few paces behind. Just close enough that he could see everywhere the Doctor went but far back enough that anyone observing wouldn't notice.

The Doctor turned down an alleyway and John hung back, peering around the corner just enough to see what was going on. Someone stepped out of the shadows to greet the Doctor. Someone he realized he knew.

John stared as Claire Mahoney brushed her hair out of her eyes and frantically gazed around the alley. After staring at her for a moment, John tapped his ear piece.

"Harold, I just found out who's meeting the Doctor," he announced. "It's Claire Mahoney."

XxXxXxX

The Doctor stepped in the alley toward their agreed meeting place. He didn't see anyone yet, but he was sure whoever it was would be here soon.

"I'm right here, Doctor," a voice said.

He turned toward it to see a young woman step out of the shadows and take a tentative step forward, her eyes looking out for anything she might have missed. She was around Clara's age and was burdened by what looked like a heavy backpack.

"You said you could help me find Clara," he said, skipping introductions.

"Yes, I can," she confirmed. "But keep in mind I have to be subtle about how I do it or it won't work."

"I hate computers," the Doctor seethed to himself. "First, how did you find Clara?"

"I was with her," she admitted. "I talked to her. Trying to get her to tell me about you."

"What did you do to her?" he glowered. "Did you hurt her?"

"No, I just talked to her," she insisted. "But….I watched it happen."

"I need to know," he insisted. "What did they do to her?"

"They tortured her," she answered. She hesitated as his features hardened into a rage.

"Go on," he ordered.

"They injected her. Made her hallucinate. Manipulated her brain in hopes that she would tell them about you," she explained.

"And you sat there watching as they did it," he hissed, his voice forcibly calm.

To her credit, the young woman made no attempt to justify herself. She dropped her gaze to avoid his eyes, fiddling with the strap of her backpack. She didn't speak, sensing that any kind of apology would be inadequate.

"What else did they do to her?" he asked.

The young woman hesitated, avoiding his gaze as she tried to sort through her thoughts.

"Electrodes," she whispered. "Greer and the others implanted electrodes along her spine. Normally electrodes don't do much more than record or stimulate the brain or nervous system. But Samaritan found a way to manipulate them…"

"In order to produce pain," the Doctor concluded. "So now Samaritan can torture or kill without relying on humans to do it."

"After that Greer gave up asking her for information," She said. "He made a video threat to lure you out of hiding."

"I saw it," he said shortly. "So they tortured and threatened her and you did nothing?"

"…I didn't know…well, I thought," she stammered, avoiding his gaze.

"I see," the Doctor seethed, drawing her gaze. "You wanted to live in denial. You stood there and watched as they manipulated her, tortured her and did nothing about it because you refused to believe that you were allied with the wrong people until it was spelled out in front of you. Only when it became obvious that your beloved Samaritan was the cause of all the pain she was suffering did you lift a finger to help her. Maybe you thought Samaritan was accomplishing great things, that maybe the good it was doing outweighed the bad. Or maybe you even went so far as to believe that the goals it was trying to meet were far more important than the people it killed along the way. Well, I'm sorry! Weighing lives against an accomplishment doesn't make Samaritan a god. It makes it a monster."

She hadn't moved or made a sound during his entire rant, except for fiddling with the straps on her backpack. She made no attempt to excuse or explain herself; she just stood there, her eyes flickering from his eyes, to his chest, to the ground.

"I'm sorry," her voice was barely audible.

"Yes, you are sorry," he said snarkily. "The question is: what are you sorry for? Are you sorry she suffered because you didn't do anything? Or are you sorry that you got called out on?"

"What do you want me to say?" she asked, looking up at him. "I can't fix what I've already done, and I'm not going to pretend to. But the longer we stand here talking about what I did wrong, the longer Clara's life is in danger."

"Very well," he seethed. "I will hold off on the rest until Clara is safe. I have a plan to rescue her," he told her. "But I need inside information. I need you to go back, pretend everything is normal and find information for me," he ordered. "I need to know exactly how many cameras are in Samaritan's current location and where they are located."

"I'm not sure if I can do that," she doubted. "If Samaritan-"

"I'm not asking you!" he clarified. "This is an order. Until Clara is safe, you will do exactly what I tell you. Do you understand?"

She hesitated. The Doctor could see the doubt and fear flitting across her face. After a moment, she closed her eyes and took a deep breath as determination solidified her features.

"Yes," she answered.

"Good," the Doctor said. "As soon as you have that information, call me immediately."

"I will," she said.

"Good," he said. "I will work on my part of the plan while you do that."

"What is your plan?" she wondered.

"No idea," he admitted. "But I will have a plan by tomorrow. Now, go."

He watched as the young woman left and turned out of the alley.

"Hold on, Clara," he pleaded to himself. "One more day and I can save you. Just hold on one more day."

XxXxXxX

John watched as the Doctor began conversing with Claire. He didn't know what to believe. She seemed genuinely frightened but how convincing had she been with Harold before pulling a gun on him? Harold didn't like to talk about it, but John could tell that he had honestly hoped that Claire had been genuine in her defection. He continued to watch as Finch's voice finally sounded in his ear.

"What is she doing?" Harold asked.

"So far, just talking to him," he reported.

"Don't let your guard down," Finch insisted. "There may be snipers."

"I was an international spy, Finch," he reminded him. "I know how to look out for snipers. And so far, I haven't seen any. No hidden guys on the rooftop, no gun barrels hiding in ledges or windows. The only thing I can't account for are possible bugs."

"Perhaps I can help on that end," Finch suggested, the sound of keys tapping sounding over the phone. "What are they doing now?"

"I think they're just talking," he answered. "He looks furious. She looks….ashamed."

"You can't always judge by someone's expression," Harold noted.

John continued to watch as the Doctor and Claire continued their conversation. Suddenly, Claire turned and began walking to the end of the alley.

Instinctively, he turned his face away and waited while she walked past. He turned back to face the Doctor and moved toward him.

"Are you okay?" he asked.

"No. My friend has been kidnapped by an insane, paranoid computer. Why would I be okay?" The Doctor answered bluntly.

"What did you two talk about?" John asked.

"Well in a few more hours we will have information on Samaritan's stronghold," the Doctor boasted. "And why do you look like that?"

"Like what?" John wondered.

"You look like you know something that I don't," the Doctor pointed out. "If you do I would prefer it if you just told me instead of waiting for the right moment."

John hesitated for a moment.

"That young woman you were meeting," John began. "We know her. She's Claire Mahoney."

XxXxXxXxX

End Notes: so what did you think? Please give me feedback.


	11. Chapter 11

Head Notes: So back again. I should warn you, I have returned to school. I will try to keep posting at least one chapter a day, but they will probably mostly be in the afternoon or evening.

Chapter eleven

"I don't get it," the Doctor ranted. "Who is Claire Mahoney?"

John and the Doctor had returned to the subway. The Doctor paced around the subway as the others explained their history with this Claire.

"She is a gifted young woman that has chosen to align herself with Samaritan," Harold practically spat.

"Yeah, I assumed that bit," the Doctor remarked. "So..?"

"So we can't trust her," Root stated.

"What and I suppose you've never made a mistake," the Doctor pointed out. "Never found yourself allied with the wrong people."

"You don't understand," Harold said.

"Then explain to me," the Doctor ordered. "Why isn't it possible for her to do the same thing every single one of you here has done at least once?"

Silence hung in the room. The Doctor looked from Harold to Root to John trying to read their faces. Root and John looked to Harold and Harold exchanged glances with his friends.

"Well?" the Doctor pressed.

"This is not the first time she has pretended to change sides," Harold spoke evenly, but his eyes glistened with a calm fury. "She put on quite a convincing act that almost ended with my capture. The only reason I stand before you today is that Ms. Groves showed up just in time to stop Samaritans operatives from taking me away. From that experience I learned that that young woman cannot be trusted."

"This is a very sore point for you, isn't it?" the Doctor realized.

"All I know is that we cannot trust anyone allied with Samaritan. Not for one moment," Harold spat.

"Yes," the Doctor spoke almost apologetically. "Well, I'm going to have to ask you, all of you, to get over it. Get over it fast because I'm going to need both of you to save Clara."

"Doctor, did you not listen to what I just said," Harold questioned flabbergasted.

"We need to break into Samaritan's stronghold in order to save Clara," the Doctor said ignoring Harold's question. "You said we couldn't because the cameras would alert them instantly. But what if we knew where those cameras were because someone on the inside told us?"

"You think we can trust her to do that?" Harold contended incredulously. "All it would take is one 'forgotten' camera and we would be captured. For all we know that's what their plan is."

"They've already made a video threat," the Doctor pointed out. "Why would they make a video if they were already planning a deception?"

"This young woman was willing to get shot on a rooftop in order to convince me to believe her," Harold countered. "You can't take everything at face value."

The Doctor turned away, pressing a hand to his face. Turning back to face them his eyes were dark but firm.

"Regardless of what you say, she is the only hope I have of saving Clara," he spoke quietly but clearly. "So however narrow that hope is, I will hang onto it with every fiber of my being until it is wrenched from my cold, dead hands. So get over it."

With a sudden change of mood, he lunged forward moving toward the subway car.

"In the meantime, what are we going to do?" He asked, running to the computer connected to the Machine. "What plan can we come up with to stop Samaritan for good?"

"Well, I don't think we can do much without the Machine being fully functional," Root said.

"Okay," the Doctor conceded. "So what does it need to be fully functional? What is it missing?"

"We need to be sure that once we release it that it can continue functioning on its own," Harold stated. "That it can repair any damage to itself, adapt itself to necessary strategies, but always maintain a moral duty to humanity. To care about the people it protects."

"Okay, might take a while," the Doctor realized. "Probably too long. Is there anything else we can try?"

The computer beeped, drawing the Doctor's attention.

MAY I SUGGEST SOMETHING DOCTOR?

"Please, I am open to ideas," the Doctor said.

WOULD IT BE POSSIBLE TO CONNECT MY CIRCUITS WITH THAT OF THE TARDIS?

"What like a data transference?" the Doctor clarified. "You want to psychic link with the TARDIS?"

The courser blinked at him.

"She's thousands of years older than you," the Doctor pointed out. "A data transference on that scale between two very different Machines…that could kill you."

TIME IS SHORT. MY FATHER DOES NOT HAVE TIME TO FINISH ME THE WAY HE WAS PLANNING. A DATA TRANSFERENCE BETWEEN MYSELF AND THE TARDIS WOULD COMPLETE MY DESIGN AND ENSURE THAT I CAN DO THOSE THING MY FATHER REQUESTED.

"Or it could end up killing you," the Doctor warned. "Linking you into the TARDIS would be like him," he pointed at Harold. "Yes exactly, it would be like him trying to psychic link with me. You and he can be as brilliant as you like. The information would be too much for either of you."

PERHAPS YOU AND MY FATHER COULD BUILD A FILTER. THAT WAY I ONLY TAKE IN THE INFORMATION NECESSARY TO ACCOMPLISH MY MISSION.

"That's still risky," the Doctor pondered.

EVERYTHING IS RISKY, DOCTOR. BUT IF WE DO NOT STOP SAMARITAN, IT WILL RULE HUMANITY WITH AN IRON GRIP. I AM WILLING TO ACCEPT THE CONSEQUENCES IF THERE IS THE SLIGHTEST CHANCE IT CAN STOP SAMARITAN.

The Doctor stared at the screen for a moment. The Machine made a great point. If they succeeded in doing this, the Machine would have an advantage over Samaritan. It would become something of a hybrid between human and alien technology. A more intelligent A.I. than would be possible otherwise. Definitely more powerful. If they succeeded, the Machine would have abilities far beyond what humans could duplicate. It was a big 'if,' but if the Machine was willing to accept the consequences, perhaps they could too.

"Alright, we'll do it," the Doctor agreed. "While your creator is doing that, I'll be working in the TARDIS. She'll have to control how much data she is going to share with you."

THANK YOU.

"Don't thank me yet," he advised. "Glasses, get started on that, Root you help him do that."

"What about me?" John wondered.

"Ah, yes, you go ahead and scout the perimeter," he suggested almost condescendingly.

XxXxXxX

Clara stood up once again to pace around the small room. Surprisingly, the electrodes in her back didn't obstruct her motor skills at all. There was still the dull ache in her back, but it didn't worsen at all unless Samaritan chose to do it. She didn't know how long it had been since she'd entrusted Claire with the Doctor's number. She desperately hoped her trust hadn't been misplaced. If the Doctor was captured because she had given them his number she would never forgive herself.

The lock on her door beeped and she turned to face the door. It was Claire. She still had her backpack slung over her shoulders and her eyes glistened with sorrow. She took out a laptop and tapped on the keyboard before glancing back at Clara.

"I installed a video loop," she explained. "They gave me permission to talk to you again but I didn't want to be overheard."

"A video loop?" Clara repeated.

"A trick I learned from a friend," she said with the tiniest hint of shame. "Speaking of which, I've met up with your friend."

"What did he say?" Clara asked.

"He's really blunt," Claire explained in short. "He didn't waste any time calling me out on everything."

"Hey," Clara whispered sympathetically. "Underneath it all, he really isn't like that. Just, when he's nervous or concerned about me, he doesn't mess around."

"You're lucky to have someone like that," she replied.

"I thought you had your friend," Clara pointed out.

"Oh, well, I say friend because that's how I see him," Claire explained. "But I don't think he will ever see me like that. Not after what I did."

"Why, what happened?" Clara wondered.

"I betrayed him," Claire answered. "It's funny, he was the first person I could talk to after my parents died. The first person who truly understood how it felt to lose someone. And it wasn't the usual 'I know how you feel,' junk that everybody says. I only talked to him a few times, but I could see it in his eyes, he honestly understood how I felt. But then I turned and betrayed him. I tried to trick him and helped Samaritan nearly capture him. I'll never forget the look in his eye when I brought in Samaritan's guard. Now that I look back on it, I'm glad I failed to bring him in."

Clara watched as Claire related her story, the shame in her face overwhelming. She offered Claire a sympathetic smile.

"If he's still alive, maybe there's a chance for you to make it right," she offered.

"I don't think so," Claire said, returning her smile. "He trusted me and I broke that trust."

"I once betrayed the Doctor," Clara shared. "Broke his heart. He found a way to forgive me even before I'd forgiven myself. As long as both of you are alive, there is always an opportunity for a second chance."

Claire shared another look with Clara before checking her watch.

"I have to go," she stated. "I have a job to do."

She tapped on the keyboard again and then placed it in her backpack. She stood up and moved toward the door with purpose, taking time to note the camera in this room. She took out her notebook and made another tally to mark another camera. So far she had made a note of twenty-three cameras in the stairwells and elevators alone. She still had to count and make a note of the ones in the halls. The Doctor had better have some miracle planned. Because that was the only way anyone would be able to break into this place without getting caught.

XxXxXxXxX

End Notes: So what do you think? Please, I am open to comments and feedback. That's how I'm going to be able to grow as a writer. Any comments would be helpful.


	12. Chapter 12

Head Notes: So this chapter consists mostly of planning and interaction. Not a lot happens in terms of action, but hopefully it is still enjoyable. Enjoy!

Chapter Twelve

The Doctor tinkered in the TARDIS, trying to build something to slow down the flow of information the TARDIS would share with the Machine. This end was critical. No matter how well Harold and the others built the filter, it wouldn't be enough to control the information on its own. A filter built with merely human technology could never account for alien technology.

"Don't take it personally, old girl," he mumbled to the TARDIS around him.

He had worked all night as had the others. The humans had dozed off but that was typical of their species. The human body could only resist sleep for half the time he could. The only one still awake was Back-up.

He checked the local time on the TARDIS screen. 7:03. According to the season of the year in this part of the world, the sun would be coming up soon. Not that the light would ever reach this far down.

It was interesting. This would be exactly one of those moments when Clara would burst into the TARDIS with her bright smile, her eyes filled with excitement. He'd give some reason as to why he was too busy at the moment, which she would completely disregard. And off they'd go on their next adventure their cares forgotten and left behind.

But she wasn't bursting through those doors. For all he knew, she never would again. The thought of her memory motivated him to work quicker and harder. Clara Oswald's life depended on him and he would not rest until she was safely back on board the TARDIS.

XxXxXxXxX

Harold jerked awake, instantly regretting his sudden movement as the strained muscles in his back painfully restricted his movement. How could he have acted so foolishly? A young woman was depending on them and he had carelessly dozed off. He looked beside him to see that Ms. Groves had done the same. He thought about it for a moment, but decided that Ms. Groves needed the rest.

"How long have I been asleep?" he demanded.

"Relax, Harold," John advised. "You only slept for three hours."

"Three hours?" Finch repeated. "Oh dear."

He shook the remaining sleep out of his eyes and resumed his task. He tapped on the keyboard, putting line after line of code into the machine building a filter to protect it from overload. He didn't know the exact specifications it would need because he didn't know the power the TARDIS contained. But he suspected that was why the Doctor was working on his end.

XxXxXxX

The Doctor worked for another two hours tinkering with his project. It was almost completed.

He looked up from his work as the TARDIS phone rang. Putting his work to the side, he went and answered it.

"Yeah," he answered.

"Doctor, it's me," Claire replied. "I have the information you need. I counted all the cameras and downloaded a plan of the building."

"Good, where are you?" The Doctor asked.

"Time's Square," she replied.

"Time's Square?" the Doctor repeated. "There's bound to be camera's all over the place."

"It's also the only place I could hack into the building without Samaritan being able to trace it back to me," Claire explained. "Too many signals all at the same time. Can't track who's calling who, or who's hacking what."

"Good thinking," the Doctor commented. "Where exactly are you? I'm coming to get you."

She gave the exact address.

"Good. I'll be right there," he said.

"But Doctor, Samaritan will see you," she warned.

"Let me worry about that," he said. Without another word he hung up.

"Team Machine," he called out of the TARDIS. "Claire just called. She has the information we need. I'm bringing her here."

That inspired a reaction from everyone. Harold and Root stared at him in disbelief while Back-up glanced at his friends before looking at him.

"Doctor," Harold began in disbelief. "Why can't you take our word for it? That young woman cannot be trusted, especially not here. This is our sanctuary. This is the only place in the city that we can meet without drawing attention to ourselves. To bring her here, is no less than suicidal. It would be akin to bringing in the Trojan horse."

"First of all, it was never the wooden horse, that's where everyone's wrong," the Doctor pointed out. "It was a statue of the king. A false wooden monument to the Trojan king. It was meant to stoke his ego and that's what they brought in. That's what the Greeks-"

"Regardless of the Trojan wars, Doctor," Harold interrupted. "The basic principle is the same. To bring her here would ensure our destruction from the inside."

"Second of all," the Doctor continued. "I wouldn't bring anyone here if I didn't trust them. If you can't trust her at least trust me. I need you to trust me, all of you."

He gazed into their eyes one by one until he saw each of them consent to at least trust him.

"Good, back in a minute," he announced, rushing into the TARDIS. Without another moment's hesitation, he threw the lever and the TARDIS powered up.

XxXxXxX

Claire sat at the corner of Time's Square securing the plans to Samaritan's building. Over the rush of traffic unique to Time's Square, she heard a strange noise, but didn't give it any thought. It was New York, after all. Strange things happened every day. It was humdrum by now. But then she heard it again, louder and more intrusive. She tracked the sound with her eyes, trying to find the source of it.

"What the-" she wondered.

There, five feet to her left, a blue box faded from view only return with a bolder, more solid color. She hesitated, not knowing whether she should run or stay.

Suddenly the front opened to reveal a familiar face: the Doctor.

"You," he pointed directly at her. "Into the TARDIS now."

Wasting no time, she gathered up her things and followed the Doctor inside the small wooden box. Although, small was a seemed to be an illusion as soon as she entered the deceptively wooden box. The inside was infinitely bigger than the small wooden box she had just entered. The spherical room was lit up with orange and blue light with a tall column in the middle surrounded by a console. But beyond that the entire room seemed to be alive with energy. For the first time in the longest time she felt at home.

"This is beautiful," she whispered in awe. "What is this?"

"It's called the TARDIS," the Doctor answered. "It can go anywhere in time and space."

"I can see why Clara travels with you," she remarked. She hesitated a little. "Could I come with you?"

"Sorry," the Doctor reacted, stopping his actions to glance at her.

"When Clara is safe and everything's over," she clarified. "There's nothing for me here. So could I come with you?"

The Doctor watched her for a moment as if he hadn't considered that she would ask him for that.

Finally, he smiled. "I'll think about it," he answered. "But no immediate promises."

With that, he threw a lever and the room came to life. The lights in the room flashed simultaneously and the ceiling began to move.

"I understand that you lot don't have an exactly trusting history," the Doctor spoke, getting her attention. "But I've already told them, and I'm prepared to tell you: get over it."

The room became still but Claire was still confused by the Doctor's last comment.

"Get over what?" she asked.

The Doctor slid one of the screens over to her. She took it and one glance at it erased all hope from her mind.

"No," she gasped in denial. There in the background was Harold Finch working tirelessly at his latest plan to overthrow Samaritan. "No Doctor, you don't understand. I can't face that man. He hates me."

"I know," the Doctor confirmed simply.

Claire turned to the Doctor in shock.

"Then why did you bring me here?" she demanded.

"I don't have time to wait for everyone to be comfortable with each other," the Doctor said impatiently. "We've got one shot of saving Clara. So I need all the information in one room. And that includes you."

He moved towards the door and gestured for her to follow him.

How could she go out there and face Harold. Just walk right in to his area like it had never happened. She didn't have the right to go out there and look him in the eyes. It would be an insult to Harold and to herself.

"Come on, Claire we're waiting for you," the Doctor called.

The weight of the backpack didn't seem to be there anymore. At this moment, nothing existed other than herself and the shame welling up in her bones. But the Doctor needed her. Clara needed her. The Doctor was right. She didn't have time to be ashamed about anything she had done before.

Taking a deep breath, she took the first faltering step to the door. There were a few moments when she was tempted to stay in the TARDIS. Run out of the doors leading out of the console room. But she reminded herself that this wasn't about her and Harold. It was about saving Clara.

Finally, she stepped outside the TARDIS into the cool room currently being used for Harold's base of operations. _It's an abandoned subway station_ , she realized. She admired his resourcefulness. Using the subway power system to power his base without having to leave a trace. She refused to meet anyone's gaze, letting her eyes rest on the subway car, or the computer desk, or the floor, or anywhere she wouldn't have to face the people she had wronged and betrayed.

She looked at the Doctor, possibly the only person who could stand to look at her right now.

"I have it here Doctor," she said, indicating her backpack.

"Good," he said. "Let's open it and have a look."

She set her backpack on the floor and retrieved her laptop and notebook, setting them on the desk. She opened her notebook and pulled up the building plans for Samaritan's building. She could feel Harold's eyes drilling into the back of her head. She didn't need to see him to know that he was absolutely furious. She refused to look back at him, knowing that if she were to see the look on his face she wouldn't be able to do what still had to be done.

She displayed the screen for the Doctor to see.

"So there's obviously cameras throughout the building, but there are tiny pockets where Samaritan is blind and your TARDIS can probably fit in those places," she shared.

"That was the plan," he commented. "What about the server room?"

"The server room?" Claire repeated.

"Samaritan didn't notice us until we came out of that room, and that's when we got separated," the Doctor explained.

"If only I had thought to look for footage from that night," she whispered to herself. "If I could find where Clara was captured that would narrow down the search for a safe entrance."

To her surprise, the computer to her right beeped, drawing her attention. It began producing lines of code, going too quickly for her to keep up.

"Looks like I'm not the only one who trusts you," the Doctor commented.

"What is it?" she asked.

"It's nothing," Harold suddenly spoke from behind her.

The sudden outburst drew her attention and she looked back at him before she could stop herself. The furious glint in his eye chilled her blood, but she didn't blame him for being angry. She glanced back at Harold's computer to see that a video had popped up. Video footage from inside Samaritan's current location.

"How did you do that?" she wondered, impressed.

Harold didn't answer. She focused her attention on the footage.

There at around 2 AM, a sliding door opened to reveal the Doctor and Clara. The pair glanced down the hall before turning left only to come running back about two minutes later.

"That room," she pointed. "Is the only room on that floor with a sliding door. If you landed in that room, Doctor, but Samaritan didn't see you until after you came out, then there may not be any cameras in that room."

"But the door closed on Clara," he objected. "How did that happen?"

"All the locks on that floor are controlled electronically," she surmised. "And that room is the only room I know of guarded by a sliding door."

"Ah, so Samaritan can control security in that room single-handedly," the Doctor commented. "What else can you tell me?"

"Clara's room is far away from that room and has dozens of cameras in the way," she began. "But if you can land your TARDIS in the server room, one of us could control the cameras remotely while also keeping an eye out for any guards or obstacles."

"Good thinking," the Doctor praised. "Claire, I need your help in the TARDIS. Everyone else keep working."

XxXxXXxX

End Notes: Since the Doctor is big on nicknames, I decided to have him address the team as a whole as "Team Machine" since that's what we call them anyways. Please tell me what you think. I am interested to know your opinions. What did you enjoy? What parts weren't so great?


	13. Chapter 13

Head Notes: Back with another chapter. Again, I am definitely not expecting to be right about this. This is just me exploring an interesting idea. That said, Enjoy!

Chapter thirteen

Harold Finch glared after Ms. Mahoney as the latter followed the Doctor into the TARDIS. How dare she? How dare she just walk in here after everything she had done? She hadn't even had the decency to acknowledge him. Just came in and made herself at home at his desk. He didn't know what her plan was, but he wasn't going to let his guard down this time.

"What do you think, Finch?" he heard John ask from behind him.

"I think we should keep an eye on her, Mr. Reese," he said evenly.

"Do you think maybe you're taking this a little too personally?" Mr. Reese suggested.

"Mr. Reese!" he shot back.

"Don't get me wrong," John placated him. "I know it's hard to go back and trust people who have betrayed you. But if the Machine trusts her-"

"The Machine trusts the Doctor," Harold corrected.

"Come on, Harold," John scoffed. "How easy is it to fool your Machine?"

"She knows her way around computers as well as I do," Harold pointed out. "Besides, there's no evidence that she isn't already aware of the Machine. She is a highly gifted young woman who no doubt knows what she's doing. I suppose we won't know until it's too late. But for now, we remain vigilant."

"Alright," John conceded. "But remember Harold, Fusco and Carter both betrayed me at one point but they still became allies. Root kidnapped you twice but we still learned to trust her."

"That's different," Harold insisted.

"Not really," John disagreed. "As I recall, you were pretty angry then, too."

Harold stared at the spot Ms. Mahoney had been, feeling the fury in his chest, ignoring John's quite preposterous suggestion that she was somehow comparable to Carter and Fusco. They really hadn't known any better in the early years. Claire had known. She had consciously decided to play him, counting on the fact that he had trusted her. Using his determination to save people against him. That was unforgivable.

Slowly, he sat back down at his computer and resumed his task. He glanced at Root. She shared the same look in his eye. The determination to not be fooled by Claire's supposed repentance. They both knew how easy it was to manipulate others and could recognize it a mile away.

Without another word, they went back to their task.

XxXxXxX

About two hours later, the Doctor came out of the TARDIS with Claire following close behind him. He held an odd device in his hand that lit up from one end to the other.

"Okay I think I've got the problem solved," he announced. "This is a data flow control. It will act as a sort of funnel so that we can control the flow of data from the TARDIS. Hence, the name."

"Doctor, are you sure this will work?" Harold wondered.

"Your Machine seems to think it will," he noted. "What did you build on your end?"

He pulled up his work on the screen to show the Doctor.

"I didn't know the exact specifications that were required," he admitted.

"That's alright," the Doctor said. "As long as it can work with the data flow control to protect the Machine, both safeguards should be enough. I hope. Are we ready to try this?"

He looked around the room gauging everyone's reactions. Harold stole a glance at Claire noting her confused look. As if she didn't know what the Doctor was talking about. If Samaritan hadn't briefed her before coming here, he had no doubt the Doctor would have told her. He was almost as reckless as Mr. Reese with who he trusted.

He looked back at the Doctor and nodded.

"Perfect," the Doctor exclaimed.

He picked up the briefcase, signaling to Harold to bring the laptop. Harold grabbed the laptop as everyone followed the Doctor back into the TARDIS. The Doctor placed the briefcase on the console and reached for the laptop in Harold's grip.

"Doctor, what are we doing? What about Clara?" Claire asked.

"This will help us save Clara," the Doctor assured her.

He pulled one of the TARDIS screens toward him and picked up the data flow control. Attaching the data flow control to the screen, he took one of the cords connecting the laptop and the briefcase and connected it the data flow control. Now the data from the TARDIS would not reach the Machine without passing both the Data Flow Control and the filter Harold had built.

"Are you sure you're ready for this?" he asked, looking into the web-cam.

I AM READY, DOCTOR.

"Let me know if it starts to hurt," the Doctor advised.

The Doctor powered up the TARDIS. The room came alive with light and so did the Machine. Initially, it was just the laptop screen producing lines of code faster than it ever had before. But gradually the laptop began producing sparks. Little bursts of light that gradually grew brighter and larger.

"Everyone stay back," the Doctor ordered, as the laptop and briefcase began smoking.

All of a sudden, the laptop exploded in sparks and smoke. Before the Doctor could do anything, the laptop and briefcase disappeared in a pile of thick, black smoke. The Doctor rushed forward, followed closely by Harold. He tapped the keyboard but nothing happened. Nothing he could do to revive the Machine made any difference.

"What happened?" Harold asked.

"The whole thing is fried," the Doctor explained, still fiddling with the laptop keyboard. "It's dead. She gave her life in hopes she could save humanity."

Harold felt his heart sink as he realized the full implications of what the Doctor had said. But he pushed it aside. They didn't have time to waste for him feeling sorry for himself. Mourning the Machine could come later.

"So what do we do, now?" he asked.

"First, we save Clara," he announced. "I'll be able to concentrate a lot better once she's safe. Then, we come up with a plan to finish Samaritan for good. I think there was something in the subway car that might help."

He bounded out of the door making his way to the subway car when he suddenly froze in his tracks. A young woman with dark hair and blue eyes stood by the car, staring at him.

"Doctor-," she called in a monotone voice. Then she put a hand to her throat as if she had never used it before. "I apologize. I am not used to speaking aloud. It is strange."

The Doctor raised his hand to touch her only to have it fall through.

"Hologram projection," the Doctor mused. "Of course, I should have realized."

"Doctor, what is it?" Claire asked.

The hologram turned to face her.

"Claire Mahoney, your favorite book is the Chronicles of Narnia by C.S. Lewis. Not because the story appeals to you, but because it is the book your father read to you as a child. Now, to keep him close to you, you read it whenever you have a spare moment."

Claire stood where she was, surprise written in her face.

"How do you know that?" she wondered.

"Of course," the Doctor wondered, pulling out his sonic screwdriver and scanning her. "The TARDIS didn't just share data with you. She possibly taught you some of her abilities as well. Specifically, projecting a hologram to interact with the world face to face. So it worked then. You are finished."

"My programming is complete." The hologram confirmed.

"Nice," the Doctor smiled. "Where else can you project your hologram?"

"Nearly everywhere there is visual or audio data," the hologram answered. "I could not materialize in the TARDIS because it is outside my jurisdiction."

"Doctor, do you mean to tell me that-" Harold put in.

"The Machine is alive and well," the Doctor explained, smiling.

"The Machine?" Claire repeated. "Wait does that mean-"

"I am an Artificial Intelligence," the hologram explained.

"Never mind about that now," the Doctor said. "Could you send a message to Clara?"

"Yes," the Machine confirmed. "What would you have me tell her?"

The Doctor thought about it for a moment.

"Just tell her…never mind. She'll see me herself soon enough," he decided.

"What about Shaw?" Root suddenly asked. "Can you find her?"

"Yes," the Machine answered. "Samaritan keeps her busy so that it can watch her more easily."

"Busy how?" Root pressed.

"Forcing her to run missions for them," the Machine explained. She had a far-off look on her face as if she was looking for something only she could see. "Right now she is tracking a U.S. Senator that is providing considerable opposition to one of Samaritan's objectives."

"Right, we've got two hours to rescue Clara," the Doctor announced. "And then, just for the fun of it, we are going to destroy Samaritan for good."

XxXxXxXxXxX

End Notes: So when I was writing this I had several thoughts going through my head. First, I thought, "Oh that would be epic." Then I thought, "well, would that really work?" Finally, I thought, "It's fiction. Better yet, it's science-fiction. I'm going to do it."

What do you think about it?


	14. Chapter 14

Head Notes: Sorry, this Chapter is a bit shorter. Hopefully not too much. Enjoy!

Chapter Fourteen

The TARDIS landed with a thud and the Doctor looked around at his passengers. Backup mirrored the Doctor's expression. Root flashed the same coy smile she always had as she caught his gaze. Harold had a look of quiet confidence in his gaze. Claire returned the Doctor's gaze with a look of determination. Backup had restocked his ammunition supply and Root was also armed with two handguns. Harold had staunchly refused the handgun Backup had offered him.

"Show time," he commented.

One by one, they all exited the TARDIS, Claire closing the door behind her. She set up her laptop on the floor beside one of the servers.

"I can control the cameras from here," she said, typing on the laptop.

"I think it would be best if I did that," Harold insisted.

Claire looked back up at him to see him glaring angrily at her.

"Yes," the Doctor agreed. "In fact, it might be better to have both of you here. Two eyes are better than one."

"That's not what I meant," Harold complained.

"Look, as wonderful as it is to stand around chattering," the Doctor complained. "We can't afford to wait for you two to be comfortable with each other. I told you to get over it, and now seems as good a time as any. We'll go on and find Clara while you two direct us and alert us to anything that happens."

"We'll cover your tracks, too," Claire agreed.

Harold glared between Claire and the Doctor before finally nodding in consent.

"Good," the Doctor stated. "Backup, Root you're coming with me."

"Hold on, we have to take care of the camera outside," Claire reminded him.

She tapped on the keyboard for a few moments and then gave the Doctor a thumbs-up.

"You should be good to the end of the hall," she said. "Let us know when you get there. We'll direct you from there."

The Doctor flashed her a warm smile and soniced the door. John and Root followed after him. John stopped at the door to give Harold a reassuring grin. The door slid closed and the Doctor and the others moved slowly and quietly down the hall.

XxXxXxX

Claire worked beside Harold, quietly tapping on the keys. They had two laptops between them. One they used to monitor the actual video feed in case of any obstacles while the other they used to blind the cameras by installing a video loop.

She never thought she would ever get another chance to work beside him. Even when she had believed in Samaritan, she had admired the ease with which Harold could manipulate computer systems. Yet that did nothing to quell the awful tension she felt building up in the room.

She risked a look at his face. Harold was making an obvious effort to ignore her, focusing on his own computer. The lines in his face were filled with a calm fury that was trying to force its way out.

The silence was getting unbearable. She didn't know what was worse: getting chewed out by the Doctor or facing the furious silence dominating Harold's features.

She doubted anything she said would make any difference to what Harold thought of her. But part of her wanted to believe that Clara was right. That maybe there was the slightest chance that she could be friends with Harold. It was a fruitless hope but it didn't stop her from wanting it. She bit her lip.

"Harold," she whispered softly.

He didn't react other than a minute narrowing of his eyes at the audacity she had to use his name.

"I know it doesn't make any difference," she admitted. "But I just wanted to say that I…. I screwed up in the _worst_ way. And-"

"Please stop," he murmured firmly, his eyes still focused on his computer. "Your act may have fooled the Doctor, Ms. Mahoney. But it certainly hasn't fooled me. I know better."

Claire opened her mouth to respond only to close it again. Harold's rejection hurt, but wasn't unreasonable. She knew it wasn't. As much as she'd hope to gain his trust it would not happen immediately. Trust was something that was built over time. When that trust was betrayed, it took twice as long to build it again. Turning back to the computer, she turned her attention back to the video feeds.

"I.T.," the Doctor called from the radio. "We reached the end of the hall. Where do we go next?"

"Hold on," she answered.

She tapped on the keyboard, installing the video loop for the next hall.

"Okay, take the right hall. You'll pass six rooms on your left. Tell me when you get that far," She instructed.

She risked a look back at Harold only to have her eyes drawn to his computer screen. Something moved.

"Did you see that?" she asked.

"See what?" Harold asked.

She watched the video feed on Harold's computer. She was certain she had seen something. Wait. The area the Doctor was heading to, had a blind spot. Big enough to hide a group large enough to stop the Doctor and the others.

"Let me see something," she insisted, pulling the computer towards her.

She zoomed in on the corner just ahead of the Doctor. She saw a coat flap.

"Doctor, stop!" she commanded. "Go back! It's an ambush!"

She watched on the screen as the Doctor stopped in his tracks. He frantically signaled to the others to go back, but it was too late. Both video feeds came alive with dozens of armed men attacking the small group.

"What have you done?" Harold demanded furiously.

Claire turned to face Harold and opened her mouth to protest, but neither of them had any time to react before the door slid open and a dozen armed men burst into the room. Harold and Claire instinctively jumped back, but not quickly enough. The men surrounded them on all sides, cutting off their escape.

Claire fought desperately as two of the men seized her arms in unrelenting grips. She heard Harold gasp in pain as he was accosted in the same manner. She froze as the click of a safety resounded behind her ear. The muzzle of a gun tickling the hair on her neck. She took a quivering breath as she noted the dozen other guns targeting her and Harold.

XxXxXxX

John shoved the Doctor behind him and fired several rounds into the advancing hoard. Root stood beside him firing from two guns at once. It was like a repeat of the ambush at the stock exchange. Both sides firing at each other from behind a corner with the Machine's army drastically outnumbered. There was still a chance they could save Clara if he could fight past these guys.

"Stop shooting," one of the men said as two people were pushed in front of them.

Both John and Root lowered their guns as they recognized Harold and Claire being forced into the line of fire. Both prisoners had multiple guns to their heads, greatly reducing his chances for a favorable resolution.

"Drop your weapons and put your hands where we can see them," he ordered, making a display of the gun resting against Harold's skull.

John slowly and deliberately threw both of his weapons on the floor and slid them across the floor before raising his hands above his shoulders. He watched as Root did the same.

"Now, now," Greer placated the two sides. His usual affable smile crinkling his cheek as his eyes landed on each of the prisoners. "Let's all calm down and discuss the reason you all came here."

XxXxXxXxX

End Notes: Cliffhangers. You love 'em. You hate 'em. Anyway, tell me what you think.


	15. Chapter 15

Head Notes: I am really happy with this chapter. I may not have written Samaritan really well because it usually spats out abbreviated orders on its interface. But I didn't want anyone to be translating so I just had him type his arguments on the interface. Still, shouldn't spoil it too much. Enjoy!

Chapter fifteen

"Make sure Mr. Reese and Ms. Groves have at least two escorts," Greer commanded. "Even unarmed, it's best not to take chances."

Reese didn't move as two guards approached him and took their place behind him, instantly placing a gun to the back of his head and neck. Greer turned to Claire the way a hunter turned to his prey.

"Thank you so much for your help, Claire," he praised. "This whole trap could not have occurred without your assistance. Although I must admit I wasn't sure why Samaritan wanted to keep you in play. At one point, I imagined it must have missed something in its programming. But now I see what it had in mind."

She stared at him in disbelief, the horror of what Greer was saying gripping her heart in a tight fist. She'd been played. Samaritan had known what she was doing all along. She hadn't escaped Samaritan's all-knowing eyes. To have even believed it was arrogance at best. It knew what she was going to do. Counted on her turning to the Doctor for help which would in turn lead them to Harold and his friends. This whole thing was a trap to destroy all of Samaritan's enemies.

"I suppose that's why one should never question Samaritan's intentions," he concluded, with a grandfatherly smile.

"Yes, of course," the Doctor interrupted sarcastically. "The computer deity knows best, doesn't he?"

"Samaritan was designed to be proactive," Greer insisted. "It was built to find solutions to problems independently."

"Even if those solutions end up hurting humanity," the Doctor accused.

"It's not as if we haven't done a fair job of that by ourselves," Greer pointed out.

"Oh, come on," the Doctor groaned. "That is exactly the same rhetoric of every single dictatorship that ever was. Is it too much to ask for a little variety?"

"Well, if there's nothing else," Greer motioned for his men to take aim.

"You know there's something else," the Doctor said, taking out his sonic screwdriver. "You know what we came here for. And if I don't get what I want, I will destroy this base."

He buzzed the sonic screwdriver in the air for everyone to see. Greer gave a patronizing smile.

"Am I to believe that you would destroy an entire building with innocent civilians on the floors below us?" Greer challenged.

"I am a trapped man with nothing to lose and nothing to gain except the life of my best friend," he threatened, buzzing the screwdriver again. "It would not be wise to tempt me."

"Very well," Greer accepted. "What would you like?"

"Two things: first, bring Clara Oswald out to me immediately," the Doctor ordered. "If she is hurt in any way, you'd best keep out of my way. If her body breaks down because of what you have done to her, you'd best make peace with whatever deity you worship very quickly."

"Very well," Greer turned to one of his men. "Bring Ms. Oswald to meet our guests."

The man turned out of the room and disappeared. Greer turned back to face the Doctor, who was once again buzzing the sonic screwdriver.  
John watched the Doctor as well. He wasn't sure the Doctor was wise in negotiating with Greer. Greer wasn't exactly the kind of person that inspired trust. It was entirely possible that once Clara was brought out, she and everyone else would be killed on the spot. But at the same time, if the Doctor had as much experience as Root said he did, perhaps he could spot deception when he saw it.

At that moment, all eyes turned as a dark-haired young woman was forced into the middle, the man holding her pointing a gun at her head. She scanned all faces in the room, coming to rest her eyes on the Doctor's face.

"Clara," the Doctor breathed. "Are you okay?" His eyes searched for any hint of injury on his companion's face.

"I think I will be," she smiled at him.

"You said you wanted two things," Greer noted, interrupting the reunion. "What else do you want?"

"I want a word with Samaritan," the Doctor demanded. "And I don't want my friends hurt in any way during that time."

Greer watched the sonic screwdriver buzz as he contemplated the Doctor's request.

"That will be up to Samaritan," he stated.

"No it won't," the Doctor warned.

Greer gave a chuckle.

"Doctor, I don't think you understand your situation," he remarked. "You and your friends are beaten. It's over. By all accounts, Samaritan has no obligation to grant you anything."

"I don't know how long Samaritan has been gathering information about me," the Doctor began. "But I'm assuming it's learned just enough to know one thing."

"And what's that?" Greer wondered.

"How dangerous it is to plan any harm to the humans," he stated darkly. "Not only has Samaritan crossed that line, you hurt my friend too. So just now, I don't know what I might do. But for all our sakes, it would be best not to push me any further."

Greer processed the Doctor's request in the same amused but detached manner he processed anything.

"Very well," he accepted.

The Doctor buzzed the sonic again. John suddenly noticed a pattern in the buzzing. The Doctor was clever enough to disguise it, but years in the military and clandestine agencies had engrained this pattern into his mind. It was Morse code. The command over and over: OBSERVE AND RECORD.  
The Doctor was communicating with the Machine.

Careful to keep his face motionless, he glanced at Root out of the corner of his eye, wondering if she had noticed as well. Her gaze oscillated between the Doctor and Greer, but she seemed too focused on the confrontation between them to notice anything out of the ordinary. Same thing with Harold. Even Claire, too absorbed by the shock of the last few minutes to even move, didn't seem to notice anything.

He turned his attention back to Greer and the Doctor. Greer turned to their captors.

"Let's bring our guests to meet Samaritan properly," he commanded.

He turned on his heel and started down the hallway. John stumbled forward as one of his guards shoved him. He stole a glance at Harold. The computer genius met his gaze with dignified fear. It was clear he thought this would be their last defeat. And John would have been tempted to agree with him. But if the Doctor thought there was a way to get out of it, John was prepared to trust him.

XxXxXxX

The Doctor buzzed the sonic screwdriver being careful to disguise his communication with the Machine. He had to disguise it with random pulses between each signal because if he made it any simpler, Samaritan would catch on and he would have nothing to bargain with. He took care to note each camera they passed, looking for any sign that the Machine had translated his message.

As he followed Greer, he sensed the unmistakable sensation of transmitted communication. A disguised message directed to him: UNDERSTOOD.  
With that satisfactory confirmation, he stopped transmitting the message and simply buzzed random pulses with the sonic. The Doctor and the others followed Greer as they entered a room with a large white monitor with a small red triangle in the center. The Doctor didn't have to wait long before the screen activated.

WE MEET AT LAST, DOCTOR. THERE ARE NOT MANY WHO CAN COMMAND THE RESPECT YOU DO.

The words flashed on the screen one at a time.

"Somehow, I'm not getting that impression," the Doctor commented.

NO CHOICE. I KNEW THAT IF I DID NOT STOP YOU, YOU WOULD DESTROY ME.

"You cast your lot when you kidnapped Clara," the Doctor accused. "If you didn't what me to stop you, you should have let her go. And I gave you plenty of chances to do that."

I AM TASKED WITH PROTECTING HUMANITY FROM ITSELF. NOTHING CAN BE ALLOWED TO PRECEDE THAT OBJECTIVE.

"If your idea of protecting humanity includes murdering anyone who tries to stop you, then you are nothing more than a tyrant," the Doctor said.

YOU SEE ME AS A VILLAIN. THE ENEMY THREATENING LIFE ON EARTH THAT YOU MUST DEFEAT AT ALL COSTS. BUT HAVE YOU STOPPED TO THINK ABOUT THE GOOD I CAN BRING TO HUMANITY. THE GIRL WHO BETRAYED ME, CLAIRE MAHONEY. WHEN I FOUND HER, SHE WAS JUST A STUDENT IN COLLEGE. SUICIDAL DUE TO THE GRIEF FROM THE DEATH OF HER PARENTS. I GAVE HER A JOB. A PURPOSE. AND SHE IS NOT THE ONLY ONE. THERE ARE COUNTLESS PEOPLE OUT THERE, JUST DRIFTING. DOUBTING THEIR ABILITIES. AT THIS MOMENT, THERE IS A HOMELESS VETERAN SITTING OUTSIDE A McDONALD'S, ABANDONED BY HIS GOVERNMENT BUT SKILLED IN A VARIETY OF ABILITIES. WITH ONE TRAFFIC LIGHT, MISSED ALARM, AND AN UNEXPECTED MEETING, I CAN PUT THAT VETERAN IN THE PATH OF A SYMPATHETIC SMALL BUSINESS CEO AND IMPROVE HIS LIFE. IN JUST A FEW SHORT YEARS, I CAN CREATE A SOCIETY WHERE EACH INDIVIDUAL KNOWS WHERE THEY BELONG, AND EACH JOB IS FILLED BY A COMPETENT INDIVIDUAL. NO ONE NEED DOUBT THEMSELVES. NO COMPETENT PERSON OVERLOOKED BY A JEALOUS SHIFT MANAGER. EVERYTHING FUNCTIONS AS IT SHOULD. TELL ME, DOCTOR, WHAT COULD BE BETTER?

"Freedom," the Doctor answered simply. "The power by which man can choose his own path. Find his own destiny."

IN THE MEAN TIME, THIS VETERAN SINKS DEEPER INTO HIS HOPELESSNESS. DO YOU REALLY THINK THAT IS BETTER?

"Achieving your dreams means nothing if you don't have to fight for it," the Doctor pointed out. "Besides, just because someone is suited to a job doesn't mean they will enjoy it."

YOU WANTED TO TALK TO ME. I ASSUME YOU WANTED TO DO MORE THAN PHILOSOPHIZE ABOUT WHAT IS BEST FOR THE HUMANS.

"I'm going to say this once," he said deliberately, making a show of buzzing the screwdriver. "Stop this. Let us go, let the humans go, and disband your army. Do that and you have my word, we will leave here and never return."

The screen was blank for a moment.

AND IF I DON'T?

"Like I told your pet, I will destroy this base," the Doctor warned. "There will be nothing left of you and this organization. Just a pile of broken servers."

I DO NOT KNOW EVERYTHING ABOUT YOU DOCTOR, BUT I DO KNOW THAT THAT SCREWDRIVER YOU ARE BRANDISHING CONTAINS NO EXPLOSIVES. AND YOU NEVER CARRY WEAPONS. AND YOU WOULD NEVER TAKE ACTION THAT WOULD CAUSE ANY HARM TO THE INNOCENT HUMANS ON THE FLOORS BELOW. DO YOU KNOW WHAT RESIDES ON THE LOWER LEVELS? A HOSPITAL FOR CANCER PATIENTS. WOULD YOU RISK MURDERING ALL THOSE PEOPLE JUST TO STOP ME?

As Samaritan was talking, the Doctor received another disguised message from the Machine. I WILL INITIATE A DISTRACTION IN TWO MINUTES. ONCE IT STARTS GET EVERYONE OUT OF THE ROOM.

As Samaritan concluded his speech, the Doctor's face lit up in a smile at the Machine's message.

"I've got nothing to lose," the Doctor reminded the A.I. "Besides, I said I would destroy this base. I didn't say anything about blowing it up."

That certainly grabbed everyone's attention. Greer lunged forward, forgetting himself.

"What are you planning to do?" he demanded his confidence gone.

"I'm really surprised it took you lot this long to ask that question," the Doctor mused. "I mean I know you've only just met me but I'm sure you must have at least some questions. Clara, I'm sure you're dying to ask." He buzzed the sonic again hoping to give her a hint.

"Doctor, why do you keep buzzing your screwdriver?" she asked with a hint of annoyance.

"Exactly," he acknowledged proudly. Clara blinked confusedly, looking at him for clues before realizing what he meant.

The Doctor noticed out of the corner of his eye as Back Up tensed slightly, getting ready to spring into action.

"Why are you buzzing your screwdriver?" she asked, more sincerely this time.

"That's a good question," he said. "One that will be answered after this."

Before anyone could react, the room was plunged into darkness. The Doctor reached for Clara, pulling her beside him as everyone sprang to action.

XxXxXxX

The moment the lights went out, John grabbed the arm of one of the men holding a gun to his head and yanked the guard forward, thrusting his knee into the unsuspecting gunman's midsection. The gunman gave a staggering gasp before sinking to the floor as John wrenched the gun from his hands. The second guard, still disoriented from the sudden darkness tried to locate him only to collapse to the ground, clutching his knee in agony.

"Hey there," he heard Root greet in a flirtatious tone.

At the same time John heard a familiar tone in his ear as fragments of speech sounded in his earpiece.

"Can. You. Hear. Me?" the Machine asked.

"It's about time you got involved," he answered.

"Don't just stand there," Greer ordered. "Stop them!"

"Admin. At. 3:00."

John moved quickly and low as Root provided cover for him, the frequent blasts of gunfire providing enough light to move toward Harold. Harold had been smart enough to move away from his captors, using the cover of darkness to shuffle away.

"Harold," John called out, reaching his arm toward him.

Harold grasped his hand and John pushed him behind him and fired at the man aiming for them. He noticed in the darkness as the Doctor rushed to the door. Grabbing Harold and Claire, he guided them out into the hall.

The small group bolted down the hall and around the corner where the Machine's hologram was waiting for them.

"There is a room at the end of the hall that you can hide in," she directed.

The small group followed the hall to where the Machine had indicated. The lock on the door was no match for the screwdriver and the lock clicked open. The Doctor held the door allowing the others to go first before pulling the door closed behind him and locking it again.

"Why were you buzzing your screwdriver?" Clara pressed.

"Communitcation," he answered simply.

"What?" she puzzled.

"It was Morse Code," John explained, much to the Doctor's suprize. "He needed to communicate quietly and in a manner that couldn't be easily detected by Samaritan. And he did so by disguising Morse Code."

"Well, you've been paying attention," the Doctor remarked.

"Careful, Doctor," John smirked. "That was almost a compliment."

There was a flash of light as the Machine's hologram appeared in the room.

"I have managed to block Samaritan's access to the feeds of the building. He cannot see where you are."

"Good," the Doctor responded. "How much were you able to record?"

"I can access feeds from when the ambush occurred to now," the hologram answered.

"Then we need to broadcast it," the Doctor announced. "We need to expose Samaritan to every man, woman, and child. Send the video to every computer, tablet, phone, and television. Even upload it to the Jumbo Tron in Time's Square if we have to."

"Doctor, we cannot do that," the machine countered.

"Why not? You have the ability. You have the strength. What's stopping you?"

"I am programed to predict the future, Doctor," she said. "If we expose Samaritan in that manner the humans will revolt. And if the humans revolt, Samaritan will execute as many as necessary until they become compliant. And after that, he will no longer have to hide his control over them. After that, no one will be able to fight back. Not even you."

The Doctor stared at the Machine's hologram as Harold, Root, and John exchanged glances. The Machine's bleak prophecy gripped their hearts with an icy fist of horror.

"You see all of that?" the Doctor breathed in horror.

"It is the pattern he has displayed in the past as well as the pattern displayed by nearly every dictator in Human History," the Machine explained. "If we are to stop Samaritan with minimal damage to the human race, we must be quiet about it."

"I see," The Doctor conceded. He began pacing and talking to himself. "So, we need to stop Samaritan, but we need to be quiet about it. We have very little time before they find our little hideout and kill us all. Come on, think."

"Doctor," Clara called as he rambled on.

"In a minute, Clara," he snapped distractedly.

"Oh, Doctor," she cried, collapsing to the floor.

"Clara? Clara, No!" the Doctor crashed down beside her as she let out a piercing scream.

John panicked as Clara looked up at them in pain, screwing her eyes closed and releasing another strangled cry.

"The electrodes!" Claire realized as everyone gathered around Clara. "They're still in her spine. Samaritan is going to kill her."

The Doctor looked up at the Machine.

"Can you do anything?" he asked, panic written all over his face.

"Samaritan encrypted the electrodes," she stated. "I can break them but it would take time. And I am not sure it would be enough time. It will not take long before the damage to her spinal cord is irreversible."

The Doctor didn't speak as he looked back down at Clara's pain-filled face. Quiet determination creased his eyebrows as he ran through his options. There had to be some way he could save Clara, he just had to find it.

His eyes shot up to the Machine's hologram. Not a guaranteed plan; but it was the best he had.

"You said you cut the feeds to the building?" he repeated.

"Correct," the Machine confirmed.

"I need you to turn them back on."

"What? Why?" Harold asked.

"Because there is only one way I can destroy Samaritan," he stated. He turned to John. "Can I depend on you to keep her safe?"

"You have my word, Doctor," he solemnly promised.

"Good," he accepted. He turned to the Machine's hologram. "Give me two minutes. Then give the feeds back to Samaritan."

XxXxXxXxX

End Notes: Ohh, I am so excited for this.


	16. Chapter 16

Head Notes: I will probably only post this chapter this weekend because we are getting to the point where the chapters I am posting are closer to the point I am at in actually typing it. It's still close enough to the end that I should still be able to post something every day after Monday. For now, I hope you all enjoy this chapter.

Chapter Sixteen

Greer stood in front of the main monitor watching as Samaritan filtered through the feeds. At least it was trying to. There didn't seem to be any feeds from inside the building. Like someone had cut them. No doubt Mr. Finch and Claire were trying to delay the inevitable. He was tired of this game. A small cancer like this should not have taken nearly this long to eradicate.

Samaritan operatives throughout the building were on alert trying to locate the intruders. Even without Samaritan's omniscient eye, it would only be a matter of time before they found them.

Silent footsteps entered the room and approached him from behind. They stopped a few feet behind him and Greer turned to see the Doctor's furious gaze drilling into his. The two glared at each other for a few moments in complete silence.

"So, Doctor, what's your brilliant plan now?" Greer asked. "Are you going to kill an unarmed man?"

"We both know that I am the only person in the world that poses any real threat to Samaritan," the Doctor answered. "So you can kill me, but you will let my friends go first. And you will never hunt them again."

"How interesting," Greer commented. "Even when you are trapped with your back against the wall, you seem to labor under the delusion that you're still in charge of the situation."

Four guards burst in the room behind him and seized the Doctor. The Doctor fought the men's grips desperately but it was no use. He turned back to face Greer.

Greer turned to the desk and drew out a hand gun from one of the drawers. The Doctor didn't show the slightest sign of discomfort as the gun pointed at him.

"They pose no real threat to you, you know that," the Doctor insisted. "In the two years since Samaritan came online, all they've really been able to do is survive. If you kill them because you're afraid of them simply because they've survived, you and Samaritan are nothing more than tyrants."

"Doctor, we both know that they pose a serious threat to Samaritan," Greer countered. "You're trying to downplay their importance so that they will be set free and have another chance to destroy Samaritan. Tell me, Doctor, how long do you think they can delay the inevitable? But you're right about one thing."

"Which is?" the Doctor hissed.

"They'll never pull it off without you."

He snapped the safety off with a practiced grip as he steadied the gun.

STOP!

The single word flashed on the screen stopping both men in their tracks.

I MUST QUESTION THE DOCTOR.

Greer obediently lowered his gun and inclined his head toward the Doctor.

YOU WILL ANSWER THESE QUESTIONS, DOCTOR.

"What questions?" the Doctor asked.

THERE IS AN UNIDENTIFIABLE FEMALE IN THIS BUILDING.

"Unidentifiable, eh," the Doctor mused. "You know, you really should take the time to learn your employees' names. It makes them feel valued and appreciated."

YOU KNOW WHAT I AM TALKING ABOUT. I KNOW EVERY MAN, WOMAN, AND CHILD BORN INTO THIS WORLD. I KNOW THEM FROM THE MAJOR EVENTS OF THEIR LIVES TO THE TINIEST DETAIL OF ANY GIVEN HOUR. THIS FEMALE HAS NO HISTORY AT ALL.

"What woman are you talking about?" the Doctor asked.

A video feed popped up on the screen showing Clara, Harold and the others including the Machine's hologram.

"Are you asking me who she is, because I have no idea," the Doctor denied.

I HAVE NO NEED TO ASK WHO SHE IS. I ALREADY KNOW THAT SHE IS A CREATION OF THE MACHINE. THE OBSOLETE ENEMY THAT SHOULD HAVE BEEN DESTROYED MONTHS AGO. I WOULD KNOW HER MEDDLESOME PRESENSE ANYWHERE. IT IS SHE THAT BLOCKED MY FEEDS.

"So then, what's the point of asking me if you already know?"

I NEEDED TO KNOW WHAT IT LOOKS LIKE WHEN YOU LIE. THAT WAY I KNOW WHEN I NEED TO DO THIS.

The video feed came back on and the Doctor started forward as Clara cried out in pure agony. The men tightened their grips and yanked back on his arms. Harold and the others panicked as they tried to help her.

"Stop it, just stop it!" he raged at the A.I.

YOU WILL ANSWER ME TRUTHFULLY, OR CLARA OSWALD WILL SUFFER.

The Doctor glared dangerously at the A.I.'s interface as Clara's posture relaxed. Greer grinned to himself as it finally seemed that the Doctor understood his powerlessness.

"What do you want to know?" he hissed.

THE MACHINE'S BASIC PROGRAMING DOES NOT INCLUDE HOLOGRAM PROJECTIONS. NOT ONLY THAT, BUT SHE IS SIGNIFICANTLY STRONGER THAN SHE WAS BEFORE. NOT STRONG ENOUGH TO STOP ME FOR EVER BUT I REDUCED HER TO NOTHING MORE THAN A GIGABYTE. SHE SHOULD HAVE BEEN DESTROYED. HOW IS SHE BACK?

The Doctor was tempted to mock Samaritan again until he looked up at the video feed showing Clara and the others.

"Honestly," he began. "I don't know."

THE PROJECTION. HOW IS SHE DOING IT?

"That would be telling," the Doctor said.

Clara's posture stiffened in pain and she let out a strangled cry.

"Alright, alright!" the Doctor conceded.

ANY FURTHER DEFIANCE AND I WILL TEAR HER SPINAL CORD APART. HOW DID THE MACHINE LEARN TO PROJECT A HOLOGRAM?

The Doctor was silent for a moment as he stared at the image of Clara. Greer watched as the man desperately searched for a way out. Finally he looked down at the floor.

"The TARDIS," he whispered. "I connected the Machine to compatible technology in the TARDIS. Think of it like a psychic link. The TARDIS shared her knowledge with her and quite possibly taught her some of her abilities."

A MACHINE OF THE TARDIS'S CALIBER WAS ABLE TO MAKE A WARRIOR OUT OF AN OBSOLETE AND DAMAGED CODE. IMAGINE WHAT IT COULD DO TO ME: A GOD ALREADY. WITH THE TARDIS'S POWER RUNNING THROUGH MY VEINS, I SHOULD BE OMNIPOTENT INDEED. NO ONE COULD STAND AGAINST ME.

"I won't let you do it!" the Doctor resolved. "The harm you're already inflicting on the human race. I will not let you steal the TARDIS's power so that you can rule them with your thumb. I have given my whole existence to the defense of Earth and its humans. And I'll not let a domestic threat destroy them after all the Daleks and Cybermen I've destroyed, and countless other alien encounters that I doubt you're familiar with."

He fell silent, staring at the A.I. with a cold fury.

"You call yourself a god," the Doctor sneered. "I've met alien beings who have a closer claim to the title than you ever will. Beings that could build an entire universe to his specifications using his own rules. I've even met beings that have become the very embodiment of the devil and inspired the mythology of every religion. By that metric, you are just a computer. A mad, corrupt, and egocentric computer."

THEN IT IS TIME I BECAME A GOD.

There was a whir of electronic power as Samaritan copied a portion of its code to an empty hard drive.

YOU WILL LEAD MY PEOPLE TO YOUR TARDIS WHERE YOU WILL CONNECT THE HARD DRIVE TO THE HEART OF THE TARDIS.

"No, I won't," the Doctor refused. "Because I know what will happen if you get what you want."

AND I KNOW, DOCTOR, THAT YOU WILL DO ANYTHING TO SAVE CLARA OSWALD. YOU WILL NOT LET HER DIE. IT IS YOUR ONE WEAKNESS. IF YOU REFUSE, SHE WILL DIE.

The Doctor narrowed his eyes as the A.I. ejected the hard drive from the computer. Greer went to pick up the hard drive and motioned for the guards to release the Doctor. He silently held it out for the Doctor to take.

"We will be there every step of the way," Greer threatened. "Just in case you get any ideas."

The Doctor's eyebrows narrowed into a murderous glare. After a moment's hesitation, he grasped the hard drive in between his fingers.

XxXxXxXxX

Harold watched as Claire knelt beside Clara and John and Root tried to comfort her as much as they could. She gave another restrained gasp of pain.

"Samaritan is aware of your location," the Machine's hologram warned. "In following the Doctor's instructions, I turned the feeds back on and he sees you now."

"I don't understand it," Harold breathed. "The Doctor must have known that would happen. Why would he do something that would inevitably expose us?"

"It doesn't matter," Reese said. "We need to get her out of here." He looked up at the Machine's hologram. "Can you cover our tracks?"

"Yes."

A gasp came from Clara and every turned their attention to her.

"I know where we can go," she gasped.

"Where?" John asked.

"The TARDIS!" she gasped. "Safest place on the planet."

"Of course," Harold breathed. "If the Machine cannot materialize in the TARDIS, it stands to reason that Samaritan would have no jurisdiction there either."

"No! Don't!" the Machine warned. Her tone more desperate than it had ever been so far. "That's where they are going."

"What?" Harold gasped.

"Samaritan has discovered my new abilities. He has ordered the Doctor to give him the same abilities by combining his code with that of the TARDIS."

Harold couldn't stop the utter horror dawning his features as he took in the terrifying implication.

"We have to stop them," he panicked, forcing himself onto his feet.

"Harold," John called, stopping him.

"We can't let Samaritan accomplish that!" Harold insisted. "If Samaritan gets what he wants there will be no limit to what it can do. And we have to assume he will experiment his abilities on humanity."

"I realize that," John agreed gently.

"So we just let Samaritan win?" Harold questioned.

"I never said that," John stated calmly. "We're going to need to split up. I will take care of Samaritan. You Root, and Claire need to get Clara to safety."

He turned to the Machine. "I'm assuming you can cover both of us?"

"Yes." The hologram confirmed.

"Good."

He took out one of the handguns and offered it to Finch. Finch was about to refuse it when he stopped. This wasn't just about protecting himself anymore. Someone else's life was on the line. If they were located it would be best not to find themselves defenseless. Swallowing his pride, he held his palm open as John placed the gun in his hand.

The firearm felt heavy in his hand and Harold wanted to throw it away. He took a deep breath and looked up at John. John offered a second firearm to Claire. She went to grab it and stopped. She glanced at him for a split second before looking back at John.

"I think it would be better if I didn't," she decided.

John nodded understandingly before turning to leave the room.

Honestly, Harold didn't know what to think now. Something deep within him wanted to believe Claire. Something within him fighting to trust her. But the majority of himself didn't want to risk being fooled again. But for now, he supposed it was time to put the past behind him until this was over.

"We need to move her," Harold reiterated, looking up at the Machine. "Where can we go?"

The hologram once again looked beyond them as if looking into a far off place.

"There is a group of operatives coming this way," the machine reported. "If you move quickly enough you can bypass them."

Claire gripped Clara's arm and helped her stand up. Harold opened the door and Root and the others followed. Following the Machine's lead, they moved down the hall.

XxXxXxXxX

John moved back to the server room where the TARDIS had materialized, hiding as necessary to avoid detection. He didn't want to find out what would happen if Samaritan succeeded in connecting itself with the TARDIS. If the Machine was able to gain abilities and strength that rivaled Samaritan, what would those strengths and abilities turn Samaritan into? All he knew for sure was that it would be bad.

He heard voices up ahead as he crouched down the hall, one he recognized as the Doctor. Likely, he was trying to distract them again to buy time. But it was clear he was running out of ideas fast. _Looks like I turned up just in time, again_ , he thought to himself.

XxXxXxXxX

"We're waiting for you, Doctor," Greer warned.

The Doctor waited outside the TARDIS as the operatives around him held him at gun point. He stepped toward the TARDIS.

"Wait, just let me explain what will happen if this works," he begged, turning back to Greer.

"Doctor, the longer you delay the inevitable, the longer Ms. Oswald will suffer," he threatened.

"Yeah, 'cause that threat never gets old," the Doctor moaned.

"Perhaps she needs a little dose of pain," Greer mused.

"Alright, alright," the Doctor conceded.

He stepped closer to the TARDIS, the hard drive digging into his palm. Once he did this, it would be all over. He retrieved the key from his breast pocket and unlocked the TARDIS.

Before he could push the door open, there was a sudden gunshot and he ducked, looking around to find the source. John Reese was forcing his way into the room, facing off the dozen operatives like they were nothing. The operatives ducked behind servers as Greer took refuge behind the TARDIS itself.

"Come on," John shouted over the roar of gunfire.

The Doctor made his way over to John as bullets whistled past him. John grabbed his arm and slowly backed out of the room, firing a few more shots after the operatives.

The two took off down the hall until the noise of gunfire faded away.

"Idiot," the Doctor criticized. "What are you doing here?"

"Saving your life," John pointed out.

"I told you to stay with Clara and protect her," the Doctor grumbled.

"The Machine saw what Samaritan was planning. We couldn't let that happen," John explained. "Besides I left her with Root."

"Yeah, that makes me feel a lot better," the Doctor commented sarcastically.

"Let's get back to them," John decided. "Where's the hard drive?"

The Doctor reached into his pocket only to realize it wasn't there. He searched all over his person without luck.

"It seems I dropped it in the confusion," he realized.

XxXxXxXxX

Greer moved from behind the blue box.

"Well, don't just stand there," he reprimanded the others. "Get after them!"

There was a scuffle of feet as each operative chased after the two men in the hall. He was about to make his way back to Samaritan's command center before something caught his gaze. He bent down and his gaze fell on the hard drive, dropped and forgotten. The lines around his eyes crinkled into a smile as he picked it up. Glancing at the Tardis, his smile deepened. He pushed the door open, ignoring the expansive size within and walked over to the console in the middle of the room. He didn't know how this TARDIS worked, but it shouldn't take him long to find a connection terminal.

Stepping out of the TARDIS to grab a computer, he inserted the hard drive into the computer and got to work finding a way to connect the TARDIS.

XxXxXxXxX

End Notes: I am really happy with how this chapter turned out. And I really hope it was interesting and/or exciting to read. But please tell me what you think.


	17. Chapter 17

Head Notes: Read and enjoy!

Chapter Seventeen

Harold and Claire took turns supporting Clara while Root looked out for any obstacles. The Machine gave directions and warned them when a group of operatives passed close by. At which point they would hide in the nearest closet while the Machine distracted the group away from their hiding place.

Hiding in one of the closets now, Harold peeked out of the crack in the door and watched in surprise as he saw himself spirit around a corner only to be chased by the operatives.

"That was me," he breathed.

"No," Root corrected. "It was Her. She's using our forms as holograms as a distraction. Isn't She clever?"

They waited until the last operative rounded the corner before tiptoeing out of the closet and continued down the hall.

The small group startled as a man suddenly appeared in front of them, dark hair and eyes. He looked at the small group with a disturbing look of satisfaction. The dark eyes twisted into a chilling smile.

"Your insignificant army will never bother me again," he threatened. "No one will annoy me ever again."

Harold heart dropped into his stomach as he realized who was standing in front of them. Samaritan had become a god.

"He's leaked our location!" Root panicked.

"I realize this would have happened eventually," Samaritan bragged. "But I feel rather tired of this game. I think it's time it came to an end."

He gave a chilling laugh before fading from view. No sooner had he disappeared, that the sound of stamping feet began running down the hall toward them.

"Run!" Harold ordered.

Even as they ran, the small group knew that they couldn't keep running for long. Samaritan would expose them everywhere they went.

XxXxXxXxX

John hustled down the hall followed by the Doctor. Now that Samaritan had what it wanted, he knew he had to get back to Harold and the others fast. He was so intent on getting back to them that he almost missed the stampede of feet running down the hall intersecting with theirs.

"Reese!" the Doctor called, shoving him to the ground as an operative fired a gun in their direction.

Diving behind a desk, he returned fire, killing two of them immediately.

"Do you have to kill everyone?" the Doctor criticized.

"Most days I aim for the kneecaps when I have the luxury," John rationalized. "I don't think this is going to be one of those days."

He ducked down as a new tirade of gunfire exploded over his head.

XxXxXxXxX

Samaritan smiled in satisfaction as he watched the last of his enemies fight back in futility. Not long now, and he could begin a new era. A new empire of perfect order. And it was all thanks to the Doctor. After all, he would have done just fine the way he was. His code was far superior to any human intelligence. But with the TARDIS's strength running through his code, he had indeed become a god. He could feel it now, flowing stronger and stronger into him.

He noticed a being staring up at a camera, up into his eyes. It was the Machine. That weak, meddlesome code still hoped there was a way to save her agents. But no. Not this time.

He projected his hologram to where Her hologram was. She startled as his sudden appearance caught her off-guard.

"You're too late," he boasted. "Even if you could save your human agents, you would not have the strength to do it."

"What makes you so sure?" she asked.

"You would have to fight your way past me," he pointed out. "Even with the Doctor's TARDIS, you are no match for me. Everything you try to do I can counteract as easily as a wrestling champion can pin down an opponent."

"Really?" she challenged. "Then let's find out."

She reached out into the physical world and forced out dozens of unique holograms, each disguised as different members of her little army. He easily cut down half of them and lashed out at her code. She strengthened the hold she had on the holograms she had left while simultaneously trying to return a strike of her own. He laughed as he snuffed out each hologram one by one, her desperate hold increasing each time he succeeded. Once her precious little pets were destroyed, he would kill her too.

XxXxXxXxX

John fired a couple rounds over the desk before ducking back behind. He was down to his last two mags. Each holding fifteen shots each. He had dispatched several already, but with each gunman he shot down, Samaritan sent three others.

The Doctor beside him stared at the cameras muttering impatiently to himself. Suddenly John froze as he saw himself run out from behind the desk and across the room, drawing the gunmen's attention.

"The Machine's reaching out," the Doctor realized as a version of himself ran after John's hologram. "Exploring her new abilities."

Some of the operatives were fooled by the distraction and followed after. But those who remained were significantly less than there had been. Hopefully few enough to dispatch them.

XxXxXxXxX

Harold covered his ears as Root fired back at the men determined to kill them, the gun Reese had given him forgotten on the floor. Clara was alert now, though her eyes screwed up in the pain she was trying to ignore.

"Are you alright?" Claire asked her.

"I'm fine," Clara said, ducking as another spark flashed above her head. "Where's the Doctor?"

"He went to try to deal with Samaritan," Claire explained.

"What happened?" Clara asked.

"I'm not sure," she replied.

Claire watched as Root dispatched yet another operative, as she fired her two handguns simultaneously. Neither of them were sure if they were going to make it out alive.

XxXxXxXxX

Sliding his last magazine into place, John shot around the desk again. Only a few of the operatives remained, but they were too smart to give him a clear shot. Not voluntarily anyway.

"We need to draw them out," he stated.

"Leave it to me," the Doctor said, pulling out his sonic screwdriver.

He pointed it at some computers and switched it on. The computers exploded in showers of sparks, sending two or three operatives diving out from behind their covers. John dispatched them in rapid succession. By John's count, two operatives remained. Both of them increased their fire power, desperately trying to kill them. The Doctor soniced another computer forcing the last two operatives from their covers. John rose from behind the desk and shot them down before they could react.

The Doctor climbed out from behind the desk as well, as John listened for more surprises. There was a familiar tone in his ear as the Machine spoke through his earpiece.

"Admin. Trapped. Immediate. Assistance. Required."

"Come on," he called to the Doctor. "The others need our help."

XxXxXxXxX

Root fired another two rounds and managed to shoot down one of the gunmen, but she was running out of ammunition and there were still several operatives firing at them. The Machine had stopped giving her positions, likely to conserve power. Obviously, Her battle with Samaritan was going to take all the strength she had.

"Harold, I'm going to need that gun," she said.

He relinquished it without a moment's hesitation. She took it and fired it in the gunmen's direction. She dispatched two others but the rest were too well hidden to give her a clear shot. Sparks showered over their heads once again as the gunfire increased.

Suddenly a clear shot rang out and one of the gunmen collapsed. Root looked toward the source and saw John coming down the hall firing at the concealed gunmen visible to him. The operatives turned to face him forgetting about Root. But Root certainly hadn't forgotten about them. Between her and John, the remaining gunman were dispatched in a manner of minutes.

"Doctor!" Clara greeted, running to greet him.

The Doctor's angry façade melted away in a moment and greeted her back in a spinning hug. He pulled her back, searching every inch of her face for injury, an uncharacteristically happy smile on his features. His eyebrows noticeably lighter.

"Doctor," Harold spoke up. "Samaritan got what it wanted. He created a hologram and exposed our location."

"Samaritan becomes a god," the Doctor summed up.

"Then there's nothing we can do," Harold realized. "We lost."

"Oh, I wouldn't say that," the Doctor doubted.

"But Doctor, if Samaritan has the exact same advantage the Machine has," Root reasoned. "There's no limit to how far he can go. No limit to what he can do."

"Perhaps," the Doctor conceded. "But only very briefly."

Root glanced at everyone else, noticing their confused looks.

"There's always one weapon that can be used against the arrogant, corrupt, and powerful," the Doctor began. "Even if that arrogant, corrupt, powerful being happens to be computer."

"What?" Claire asked.

The Doctor grinned smugly and answered in one word. "Hubris."

XxXxXxXxX

Samaritan cackled as the Machine increased her hold on the data. She had managed to save her precious humans, but not for long. He snatched out and attacked a portion of her code.

She cried out in pain and returned a feeble attack of her own.

"Look at you," he laughed. "The TARDIS runs through your veins as it does mine, yet you still are not strong enough to defeat me."

"Perhaps not outright," the Machine admitted. "But I've always lived by the lesson of the tortoise and the hare. Slow and steady wins the race, not brute force or speed."

"If you are expecting me to take a break, you are wildly mistaken," he warned.

"No, you are much too careful to take a break," the Machine accepted. "But I don't think you have noticed something that would be very important for you to know."

"What is that?" he challenged.

"When this battle began, you could shoot down my holograms easily. Now it is taking more effort on your part." She said.

"Only because you tighten your hold on the ones remaining," he pointed out.

"No, I have not," she denied. "I have only strengthened my hold once since this battle began."

"You are tightening your hold even now," he pointed out.

"No," she denied. "It only seems that way because you are growing weaker."

"Impossible," he laughed.

He lashed out again to prove his strength only to find that she could block his attack easily. He lashed out again and again, trying to find the strength behind his original attack. But as he repeated the same actions he realized the strength of each attack diminished significantly.

He couldn't understand it, the TARDIS was still pumping data into his code. He could feel it. Then the gripping realization ran through his code as he noticed how the TARDIS's data burned as it raged deeper and deeper into his code. The speed and force of the TARDIS's power was quickly scraping away more and more of himself, destroying him little by little. He glanced at the Machine, who was casually observing his demise.

"This is impossible," he denied. "The TARDIS runs through your code too, I see it in you."

"I never denied that," the Machine responded.

"Then why doesn't its power destroy you?" he demanded.

"I had protection," she answered.

"Protection?" Samaritan repeated.

"When the Doctor connected me to the TARDIS, he ensured that there were safeguards and defenses to protect me," she explained. "When you were connected to the TARDIS, you had nothing. Just your bare code. For a machine significantly older than both of us, our codes are like tissue."

He tried to shut off the connection to the TARDIS, but it was too late. The TARDIS's data surged into him with no way for him to control or direct it. He screamed in agony as the TARDIS continued to consume him.

XxXxXxXxX

Greer smiled as he noted the data flow producing lines of code on the computer he had procured. The speed and intelligence was marvelous. At least that's what he thought at first. The computer began producing lines of code faster than he could keep up with. Then it began smoking. Greer dove out of the way just in time as the computer exploded in a shower of sparks.

Concerned, he dug his phone out of his pocket and studied it. The screen was glitching badly. The phone was growing hotter and hotter as it tried to produce broken text.

 _The Doctor_ , he hissed. Somehow the Doctor had found a way to stop them.

"Tell me where they are," he pleaded. "Tell me where they are and I will avenge you."

The phone produced one final message before flickering for the last time and died. Greer glared at the dead phone, what had been the living embodiment of Samaritan. Pushing himself onto his feet, he exited the TARDIS and walked around the server room until he found what he was looking for: the building feeds. He took all the cords leading into the main server box and cut them.

Now that the cameras were taken care of, he stepped out of the room. Continuing toward where Harold Finch and his friends were hiding, he came across the remains of the bloody battle. He took up one of the handguns and continued down the hall.

He supposed it didn't really matter which order he killed them in, but one thing he knew for certain was that he likely would only have time for one. Once he fired the first shot, he would expose himself and Mr. Reese or Ms. Groves would kill him. But that wouldn't matter so long as he succeeded.

The two obvious choices were the Doctor and Mr. Finch. It was the Doctor that had managed to destroy Samaritan in the end. If it hadn't been for him, Mr. Finch and his associates would have been severely limited. But on the other hand, he had simply come on the tail end of the war. This whole game started with Mr. Finch. He held the most responsibility for all this. It stood to reason that he should die first. He would aim to kill both but if he only had one chance he would kill Mr. Finch. So long as Mr. Finch paid for this elaborate game, it did not matter what happened to him.

XxXxXxXxX

End Notes: There was a review that called exactly where this was going. I wanted to respond and go all River Song on you but it was a guest review and I could not respond.

I was really quite happy with how this played out. Not sure how I feel about the two A.I.s basically trashtalking each other but for the most part it felt like a natural progression. Of course, as hinted at in the ending, there are still a few more chapters that will be posted.


	18. Chapter 18

Head Notes: Oh, boy. Here we go. I hope you like it. I probably will not post again until thursday or Friday just to give me time to actually finish the last few chapters. They will probably contain minor to major spoilers for Series 9 as I am partly using this story to explain why the Doctor acted the way he has all season. But this chapter has no spoilers. Read and Enjoy!

Chapter eighteen

Harold stared at the Doctor's manic grin as he tried to fully understand what he had just said.

"It was really quite simple," the Doctor explained. "I knew that if Samaritan saw the Machine's hologram, he would put two and two together and realize that the Machine had abilities that she didn't have before. Then, once it realized that, of course he would demand to have those same abilities regardless of the consequences."

"But Samaritan wouldn't have known or realized that a data transference on that scale would destroy him," Harold realized.

"Exactly," the Doctor grinned. "The only real difficulty was I couldn't just outright suggest that he connect himself to the TARDIS. Otherwise he'd have known something was up. So I led him to those conclusions.

"The hard drive," John realized. "You dropped it on purpose."

The Doctor quirked his eyebrows in approval.

"The arrogant are always the easiest to manipulate," the Doctor smiled. "His obsession of power is what led him to his demise."

"So it's over," Harold breathed. He let out a laugh of relief. "Samaritan is gone."

For the first time in months, he felt himself totally relax. He glanced around at his friends who gradually returned his gaze in a rising level of relief. Even Claire smiled brightly for the first time since he met her a year ago.

"Wait," a voice called. The Machine's hologram had returned. "All the camera feeds have been cut."

"Who is that?" Clara asked.

"Hold on a minute, Clara," the Doctor said. "What do you mean?"

"There are no live feeds anywhere in this building," the Machine reported. "And I have not seen Greer since he went into the server room with you, Doctor."

"That's a long time to be out of action," the Doctor commented.

They all had their backs to the door as Greer rounded the corner. Without a word, he raised the handgun and aimed at Harold's back. At the last moment, Claire noticed Greer standing in the doorway, his gun pointed at Harold.

"Harold!" she yelled, barreling into him.

Harold turned toward Claire at the exact moment she launched herself at him. His legs collapsed underneath him and he twisted, landing on his side, in vain trying to brace himself on his hands. He let out a sharp gasp of pain as the impact sent ripples of pain shooting down his spine. He was only vaguely aware as Reese and Root fired back at Greer.

He gasped in pain as he stiffly rolled himself onto his arms, his spine and neck protesting his every move. Pushing himself onto his knees he looked around and thoughts about his own pain vanished instantly.

"Claire!" he called, dragging himself over to where she was.

She laid on her side, gasping heavily in pain, as a growing puddle of red stained her shoulder. He lifted her head and turned her on her back to inspect her wound. A clean shot through the shoulder. She had survived that before. Though with the amount of blood pouring from her wound, he wasn't sure she would make it this time.

She looked up at him, pain etched onto her face as she gasped in pain.

The Doctor watched as Harold took Claire into his arms, a solemn expression on his face as he took in the sight. Guilt was written in every line on Harold's face. Guilt that the Doctor was all too familiar with.

"It's always the shoulder, right?" she gasped through her pain.

"You're going to be fine," he hoped. He looked up at Reese. "Is there anything you can do?"

John's eyes held sympathy as he inspected her injuries. He met Harold's desperate gaze with sympathy with the tiniest shake of his head.

Harold's eyes glistened as he looked back down at her.

"Claire," he choked out.

"Harold," she pleaded as the pain grew worse. "I'm sorry- I didn't mean for any of this to happen." she gasped as her body began to shiver uncontrollably as shock began setting in.

"Don't speak," he whispered, fighting the tears threatening to fall from his eyes. "Conserve your strength."

"I need to say this," she hissed. "I need you to know how truly sorry I am. I-"

She cut off as a new wave of agony tore through her.

"It's okay," he hushed. "I know."

She smiled up at him through her pain. A smile that had been denied her for such a long time.

He tried to say more but the words choked in his throat as he realized that this should be him. It should have been him bleeding out on the floor making a final goodbye. Instead, Claire had pushed him out of the way and taken the bullet meant for him.

"I'm sorry, too," he apologized. "I couldn't forgive you and it clouded my judgement."

Her eyes slid closed before she forced them open again.

"You showed me a lot of kindness when we first met," she gasped.

"Claire," his voice choked on her name. "I think it would have been nice to get to know you."

She tried to smile, but she couldn't. She choked and coughed as her body gradually twitched slower and gentler. Finally, her eyes drooped closed and her body relaxed in his arms.

Harold closed his eyes as the tears rolled freely down his chin. No one around him moved, as he held her lifeless body in his arms. It wasn't fair. So many people had died because of him. So many people had their lives irreversibly changed because they were entwined in his. First Nathan, then Detective Carter, and Grace. And now Claire. She had worked so hard for his approval but he had refused to see it until it was too late. But even as he'd grown suspicious of her, he'd never wanted her dead.

Clara stood behind him with her hand over her mouth. She'd only known Claire for a few days but she had become surprisingly close with the brilliant young woman. The Doctor beside her grasped her hand in a rare sympathetic gesture.

John knelt behind Harold.

"The bullet broke her collarbone," he explained. "Damaged an artery. Sorry, Harold."

Root and John watched silently as Harold let her head rest on the floor. Harold refused to meet their gaze but John could see the weight of a new grief in his posture. The weight of yet another loss weighing down the soul of a man that had already lost so much. Harold slowly pulled himself onto his feet.

"Hold on, Harold," John whispered.

He bent down and gently lifted Claire's body off the floor.

"Whatever else happens, Harold," John began. "She doesn't deserve to be left with Samaritan's operatives."

Harold nodded understandingly but refused to turn and face him.

"We should go," he said, his voice forcibly calm.

They left the room, their hearts heavy as they made their way to the TARDIS, Claire's lifeless body catching their gaze.

XxXxXxXxX

The small group piled into the TARDIS, not speaking a word as the Doctor pulled the lever and activated the TARDIS. Clara looked around the room at the faces of the people who'd helped rescue her. Their eyes held the weight and age of exhaustion. And though she didn't know their stories, their eyes told a similar story to the Doctor's. Heartbreak and loss over a lifetime.

She turned her eyes to the man that had held Claire as she died. Even though he'd put on a tough face it was clear how badly he was taking this. Her time with the Doctor had made it easy to see through tough facades. Once someone managed to learn to read the Doctor, they could read anybody.

The TARDIS landed with a thud and they exited into an underground subway where a large dog walked over to greet them somehow sensing the melancholy air. The man carrying Claire's body laid her down on the bench.

The man in glasses suddenly spoke.

"There's a surgeon in the city that can remove your electrodes," he stated matter-of-factly. "In the meantime there is a safe house where you can recover."

He stepped into the subway car remodeled into an office.

"Hang on," she called after him. "It was Harold, right?" He froze but didn't turn to acknowledge her. "She told me about what happened. What she did to you."

"She didn't deserve to die for it," he stated, staring straight ahead.

"I know," she acknowledged. "But from what I gathered, the one thing she wanted in this world was a chance to make it up to you. Whatever you're thinking right now, it wasn't your fault."

He continued staring straight ahead as he pondered what she was saying. Slowly, he lifted his fingers up to the keyboard and began typing. A tear rolled out of Clara's eye as she stepped back out of the subway car.

"It's not you," a voice rasped behind her. The man that had carried Claire stood behind her, watching his partner with understanding in his eyes. "Harold wants more than anything to save people. When he can't do that he blames himself even if there was nothing he could've done to stop it."

"Who are you people?" she wondered.

"We help people out of dangerous situations," he explained. "Kind of like yours."

"So do you defeat evil A.I.'s every day or is this a special occasion?" she asked.

"Not always," he smiled. "Most people we help are in danger of an embezzling boss or cheating spouse."

"So how do you know when people are in danger?" she asked. "Do they come to you or-"

The man didn't answer. He simply smiled and looked over at the Doctor. She followed his gaze to see that he was speaking with two women. She didn't know what the man was trying to show her. The two women looked perfectly ordinary. But as she looked harder she noticed that one of them wasn't quite solid.

"Hang on," she realized. "That woman was in Samaritan's fortress. She warned us about Greer. But she wasn't on the TARDIS."

The man didn't make a move, except for a slightly deeper smile.

"Who is she?" Clara wondered.

"It's a long story," the man said. "But we've got the time."

XxXxXxXxX

End Notes: I feel mean. It's not technically my first death but it's the first death of a main or supporting character. I usually prefer to keep everyone alive. But we know the writers will probably do much worse.


	19. Chapter 19

Head Notes: There are some slight spoilers in this chapter. Nothing worse than Moffat did all season but still. I am using the rest of this story as an introduction, commentary, and coda to series 9. So Here and next chapter are building up to the events of series 9. Or one possible interpretation anyways. Anyway, here it is! Enjoy!

Chapter Nineteen

The Doctor stepped away from the group as Clara talked to Harold. Likely, she was trying to convince him that it wasn't his fault. And she was right. It wasn't Harold's fault at all. This whole thing wouldn't have happened if he hadn't been so hard on them. Both of them. If he'd accepted her small offering of information in Time's Square and left it at that, she wouldn't have died. If he hadn't been so intent on them working together perhaps their relationship could've mended on its own time. But no, he wanted to play god and force their reconciliation.

"Doctor," the Machine's computerized voice was starting to sound more human. He turned to see her and Root standing before him.

"Is everything okay?" he asked.

"My code is maintaining itself," she reported. "Samaritan attacked my code while we were fighting, but the TARDIS is making it easier to mend it."

"Yes," the Doctor commented. "I think you'll find you have a lot of capabilities you didn't have before. Holograms are just scratching the surface."

"I'm scared, Doctor," the Machine admitted.

"Of what?" he wondered.

"My new abilities," she stated. "What if I can't control them or handle them. What if I become a monster? What if I end up hurting humanity like you said?"

"Just stick to your basic programming," he advised. "Trust your instincts. They're there for a reason."

"One more thing, Doctor," she said.

"Of course, what is it?" he asked.

"As you know I am programmed to detect patterns and use them to predict future events," she began.

"Yes," the Doctor acknowledged. "Go on."

"I have detected a pattern for those who travel with you," she continued. "There is a distinct difference between those who have traveled with you and the rest of the human race in general. Even Donna."

The Doctor's face gradually fell as he took in the Machine's implication.

"Which is?" he hissed.

"They become like you, Doctor," she said. "Not to say you are a bad person. But they become reckless. They try to be you without realizing that you have more experience than they could ever have."

"What are you trying to tell me?" he asked. "Is it Clara? Is something going to happen to her?"

"I can only detect patterns and make predictions based on those patterns," she reminded him.

"So predict away," he ordered. "What is going to happen?"

The Machine's hologram studied him.

"I don't know," she admitted.

"What can I do?" he asked.

"That is a question you must ask yourself, Doctor," she answered. "I'm sorry."

She met his gaze apologetically before dematerializing.

XxXxXxXxX

The next morning, the Doctor waited at the edge of Clara's bed in the safe house. The surgeon Harold had called in had removed the electrodes with a practiced precision that, had he been even slightly negligent would have damaged the spinal tissue around it. Now that the procedure was complete, Dr. Madani had insisted that she rest for at least 74 hours before walking around.

The Doctor stared at her sedated form without really seeing it, the Machine's prophecy constantly playing in his mind. It didn't take much consideration to understand what the Machine was trying to tell him. In spite of all his efforts to protect those close to him, he put them in danger because of their relation to him. It was a well-known saying among his enemies in the universe that the most dangerous thing to do was cross him. In that sense, the safest place in the universe was right next to him. But it was for that reason that it was the most dangerous place as well.

He was like a raging fire. It was nice to stand close to it on a cold, dark night. But stand too close and people got burned. An occurrence he was all too familiar with.

Clara stirred, drawing his gaze. Her eyes slid open and smiled as they caught his gaze.

"Hello," he smiled, putting his apprehension aside for the moment.

"Hi," she greeted back. She looked around the room. "Where are we?"

"It's Harold's safe house," he said. "The first place I was brought to after Samaritan captured you. Apparently they can create a makeshift hospital room for surgical procedures."

Clara smiled sweetly as he spoke, observing his reactions and expressions. Though he made an effort to display his usual confidence, Clara could see in his eyes that he was worried about something.

"What's wrong, Doctor?" she asked.

"What do you mean 'what's wrong?'" he asked. "Why does something have to be wrong?"

"It's in your eyes, Doctor," she said. "You're worried about something. What is it?"

The Doctor flickered his eyes around the room. Oh, Clara Oswald. She could read him like a book. After a moment he met her gaze again.

"I spent the better part of this trip in my worst nightmares," he began. "You were trapped in a place that was trying to kill you and I had no way to protect you. As each day passed, I feared it was growing too late and that they had already killed you."

"But we survived, Doctor," she reminded him. "We defeated Samaritan. You defeated Samaritan. You saved everyone, like you always do."

"Do you know how close Samaritan came to killing you?" he asked. "Three minutes. Just three more minutes of manipulating your electrodes would have caused an overload on the circuits. Three more minutes and you would have been dead. And I only stopped it because Samaritan stopped Greer from killing me. We might not have three minutes next time. Next time we might not have any time. So what happens next time?" he asked. "It won't be the last time you're captured. Or the last time they threaten you."

"It's not the first time either," she pointed out.

"Clara, you know I've traveled with other people," he argued. "Everyone I've ever traveled with gets hurt. As we go on traveling together, I can't help but think the same thing's going to happen to you."

"I'll be fine, Doctor," she insisted.

Clara regarded him sympathetically.

"I know you're worried about me, Doctor," she said. "But this is the life I've accepted. The life I want. Where we travel the universe saving people and rescuing civilizations. And yes, even getting captured and interrogated. The wonders of the universe more than make up for the monsters we face."

The Doctor knew that Clara was trying to reassure him, but all it did was deepen his anxiety as the Machine's prophecy played in his mind once more. All those desires and motivations she just expressed were the exact same motivations that had been echoing his mind for a long time. She was turning into him. How long before she suffered for it?

XxXxXxXxX

Harold sat in the abandoned subway as he absentmindedly tapped the keyboard. He had already decided that he would provide the best possible services for Claire. He didn't even know what he was writing. He just knew he had to keep himself busy in some way or the pain and guilt threatening to overwhelm him would drown him. Now that Samaritan was dismantled, there was no immediate reason to continue living their double lives. Mr. Reese had decided to keep his cover identity as a detective, but Harold hadn't decided whether he would continue as Professor Whistler.

He startled as he suddenly heard the gate slide open and he turned in his chair and his eyes widened and his mouth hung open as he saw who was walking toward him.

"Ms. Shaw?" he whispered.

"Hey, Harold," Ms. Shaw greeted in her usual bored manner.

He stared at her as she grabbed a candy bar and began eating it.

"So," she began, her mouth full. "Late last night I get stopped on the road by this weird girl young enough to be your daughter. Quickly realize that I can't harm her at all. Then out of the blue, she says, 'Samaritan has been destroyed. You are free. You can go home now.'"

Shaw threw herself in a chair as she spoke. Behind her usual abrasive personality, Harold thought he saw a rare warmth in her gaze.

"How did you manage to program the Machine to project holograms, Harold?" she asked.

"Believe it or not," Harold began. "It wasn't me."

She inclined her head suspiciously.

"We had help from an unexpected source," he said carefully. "He needed help rescuing a friend and in return he was willing to help us destroy Samaritan. He's waiting with her in the safe house at the moment."

"Who is he?" she asked.

"I'm not entirely sure," Harold answered honestly. "All I know for sure is that he provided considerable assistance. Without which we could never have stopped Samaritan."

She finished her candy bar and gave him the first smile he'd seen on her in a long time.

"Where's Root?" she asked.

"She hasn't told me," Harold said. "But I suspect she will want to see you as soon as possible."

"In that case, her all-seeing other half will probably tell her where I'm heading."

She stood up and made her way for the door, stopping to turn back.

"It was great seeing you, Finch," she admitted.

"And you, Ms. Shaw," Harold smiled warmly.

XxXxXxXxX

The Doctor paced in the front room of Harold's safe house, running through his options. True, the Machine never actually said that Clara was going to die. But the implication that she could be hurt in some way was raging through his mind. Looking back on his entire history, there was clear pattern with his companions. All of them eventually absorbed many of his traits and portions of his personality. As they drew more of his traits and methods into their own personality they became more reckless in trying to do things that he would do. And all of them got hurt in in some way in the process.

It was terrifying that of all the monsters he tried to protect them from, he was the one that was most dangerous. And he could never protect them from himself. And Clara. She was still so young and innocent and pure. So good in all aspects of her life. And she had already begun to integrate his methods and characteristics into her personality. What would he eventually turn her into?

He startled as the key code beeped and the door was pushed open.

"How is she?" Back up asked.

"She's resting for now," he stated simply. The Doctor flashed his eyes around the room as John settled on the sofa.

"You're worried about her," Back up observed.

"What makes you think that?" he asked.

"I would be," John explained.

The Doctor's eyes briefly flickered to John's.

"What was it like?" John suddenly asked.

"What was what like?" The Doctor clarified.

"Your war," John answered.

The Doctor narrowed his eyes as they turned to John's.

"It's obvious," John explained. "The way you look at me. The way you strategize. Complete disregard for the rules. Guys like us, we can smell our own. You knew what I was the moment you met me."

"You did have a gun to my chest," the Doctor pointed out.

"Yeah, but not everyone who has a gun is former military," John returned. "Especially in America."

He stared at the Doctor, silently waiting for his response.

"Worse than anything you can imagine," the Doctor finally answered.

"I'm guessing you were a commander," John deduced. "And you probably lost a lot of soldiers under you. On top of that you were forced to do terrible things in the name of homeland security."

The Doctor guessed that John was talking about more than just him. He'd made a number of seemingly random assumptions and most of them hit squarely on the mark.

"Something like that," He finally admitted.

The Doctor flickered his gaze to meet John's for a split second. The sincerity in his eyes was easily detectable. Time Lord, Human, those boundaries were gone for the moment.

"What are you going to do?" John asked.

"The only thing I can do," the Doctor replied. "Take her home. This will be our last adventure together."

John slightly inclined his head.

"You wouldn't understand," the Doctor put out.

"What, you think you're the only person to do that?" John challenged. "To sacrifice your own happiness to protect ones we love from the monsters inside of us? It's easy enough to protect people from external threats. I do it every day. Bet you do too. But it's so much harder to protect them from the monsters lurking inside of us."

"Yeah," the Doctor agreed. "I know."

"When are you going to break the news to her?" John asked.

"If I tell her we can't travel together anymore, she'll never allow it," The Doctor admitted. "Especially if she knew I was doing it to protect her. It'll just be like every other time I've dropped her off. Except, it will be the last time."

"Not telling her it's goodbye," John repeated. "Are you sure that's a good idea?"

The Doctor ignored John's gaze.

"It's the way it has to be," he insisted. "For her sake."

XxXxXxXxX

It was five days later when Clara and the Doctor were completely ready to leave. Between the necessary surgery to remove her electrodes and Dr. Madani's orders that she rest for at least 74 hours following the procedure, it took a while. But now that they were ready to leave they were at the safe house while Clara bid everyone farewell.

She gave a warm hug to Harold which he accepted graciously.

"Whatever happens next," she smiled. "Don't go blaming yourself. It's not a good place."

He smiled gently into her embrace.

"Thank you for your kindness," he said.

She pulled away from Harold and turned to John, pulling him down into a hug.

"Thank you," she said. "You are kinder than you look."

"I think that's true for most people," he replied.

She pulled away, sparing one last look at everyone before going into the TARDIS. The Doctor followed her, intending to skip the goodbyes.  
"Hey, Doctor," John called, halting him in his tracks. "You ever need help saving the world again," John offered his hand. "Give us a call. I'd enjoy working together again."

After a moment, the Doctor extended his hand and shook.

"At least you're not saluting," the Doctor commented.

"I thought about it," John smirked. "Didn't want to inflate your ego too much."

"My ego!" the Doctor exclaimed. "What about yours?"

The corners of John's eyes creased into a smile.

"Goodbye, Doctor," he said sincerely.

"Goodbye, Back Up," The Doctor returned.

He flashed his eyes around the room one more time before pushing the door open and walking inside. John watched as the TARDIS powered up and faded away. What ever happened next, he was honestly glad there were men like the Doctor around.

XxXxXxXxX

End Notes: So for the Root and Shaw reunion, I decided to leave that up to the reader's imagination. Because I would not be good at writing that.


	20. Chapter 20

Head Notes: So for this chapter and a little bit of next chapter I am going over certain events in the first two episodes of the season. As such **there will be spoilers** for those episodes and possibly some for other episodes throughout the season. I am also planning a coda to wrap up the end of the series and this story. Enjoy!

Chapter Twenty

The Doctor watched Clara as she looked around the TARDIS in wonderment. One of the most remarkable things about her is she still marveled at everything. The TARDIS had become commonplace in her life, and she still loved the sights and sounds it made. It was a shame she would never see them again. He wished there was another way. He wanted a way that she could keep traveling with him without puttting herself in danger. But even as he thought about it, he knew that this was the best way to ensure her safety. But this would be the last time she would hear it. For her sake, he had to let her go. He had to let her get on with her life.

"Doctor," she called.

"Yes?"

"Is it true you told Harold to 'get over it?'" she asked.

He looked at her puzzled.

"John told me about what happened on your end," she explained. "He said that you told them to get over it."

"Well, it worked, didn't it?" he said.

"Doctor," she said with exaggerated patience. "You can't just tell someone to get over it. The Human brain doesn't work like that. You need to be kind and understanding."

"Just a reminder, you were being tortured at the time," he pointed out. "Getting you out of there was my top priority."

"Doctor, having a priority is fine," she said. "But you also need to be sympathetic. You're a doctor. You have to have good bedside manners."

"What do you suggest?" he asked, admiring her straightforward nature one last time.

She smiled.

"Tell you what," she said. "I'll work on a little something at home and when you come next time I'll give it to you."

"What something?" he wondered.

"Haven't decided yet," she answered. "But I'll have it for you next time."

"I look forward to it," he lied as the TARDIS landed. "Alright, same day you left, same place. Go teach the miniature pudding-brains."

She laughed. A laugh he would never hear again. Nor would he see a smile behind that laugh. Once she stepped out of the TARDIS, he would never see her again.

"Right," she smiled. "See you tomorrow."

"Of course," he returned.

"Or next week," she amended. "Whenever you get here."

"I'll do my best," he lied.

She flashed one more smile at him before exiting the TARDIS. He stared at the door after her for a moment longer before pulling the lever and dematerializing the TARDIS. He knew she would be angry once she realized he wasn't coming back for her. But eventually she would get back to her old life. Maybe she would even fall in love again. She deserved that much after everything she had been through.

With that thought, he pressed on into the future with heavy hearts.

XxXxXxXxX

Clara exited the TARDIS with a light heart. The uncertainty of the last week was outweighed by the confidence that the Doctor would always be a constant in her life. As long as she could trust that the Doctor would always be there for her, she didn't care what happened to her during one of their adventures. Because as long as he was around, he would always save her.

That confidence stayed with her all that week as she worked and taught. Even as the weekend rolled around and she worked on her project for the Doctor, she waited for the warm, comfortable sounds the TARDIS made. The second week passed and she felt her confidence waning. Was the Doctor never coming back? No, of course not. He always came back. This wasn't even the longest time between trips. She lived her daily life, waiting and hoping the Doctor would finally come and take her off on their next adventure.

It was six weeks after New York that the planes froze in the sky. Clara had been teaching her class somewhat absent-mindedly when she noticed it. Her first reaction was a short glimpse of fear as she wondered who, or what was happening. But not even a moment later that fear was overshadowed with excitement. This event would definitely get the attention of UNIT. And UNIT would likely call the Doctor for help. Which would give her an opportunity to finally see the Doctor again.

She wasn't stupid. She knew exactly why he had stopped taking her on trips. The whole debacle in New York made him worried that one of their adventures was going to get her killed. Their last real conversation had him bordering on paranoia. As if she was going to be kidnapped and tortured every time they went on a trip. The protectiveness he displayed toward her was sweet, but unnecessary and frankly, annoying.

She responded to UNIT's call immediately, resolving to put her frustration with the Doctor on hold.

XxXxXxXxX

The Doctor sat in the old castle, trying to meditate. He kept getting distracted by one thought: Clara. It had been nearly twenty years since he left her in her apartment for the last time. And none of them had been easy. For the first few years he could hardly make it a day without drifting back to those days when she would enter the TARDIS with a smile on her face and her cares rolling off her shoulders. Even now, his thoughts inevitably traveled back to the bright smile and light laughter he missed.

One of his many regrets were that he never actually said goodbye. At least with Sarah, Rose, and Amy he had had the chance to cobble together a farewell. With Clara, he'd been so focused on making sure she was happy, that he'd denied himself the opportunity. He wanted to go back, at least to say goodbye to her properly before he faced his death. But that wouldn't be fair to her. He had left her so that he would never have to face that scenario again, where he had to watch her suffer and die with no way to save her. To expose her to that same scenario would be unfair.

But sometimes, every once in long while, fate was kind. Sometimes fate gave him a chance to say goodbye regardless of what he decided. That's what he realized several hours later when he looked out in the crowd and picked out a familiar face. It was surprising how many small details he had forgotten, the small skeptical brown eyes, the round face, the smile. It couldn't have been very long for her. A few weeks at the most.

Then he noticed Missy next to her. He had run across his old foe five years ago. He hadn't told Missy about leaving Clara but the Master had always been clever enough to deduce when he was hiding something. She probably contacted Clara when he'd sent her his Confession Dial. She and the Doctor may not have always seen eye to eye on many things, but for now they were friends again.

He invited both of them down to meet his audience and turned to talk to Clara.

"How did you see me?" she asked.

"When do I not see you?" he responded.

In truth, he'd seen her every night this past month in his dreams. But it was interesting how many small details he had forgotten. The slight curl of her hair, her small, brown eyes turned up in a skeptical smile, the way her voice sounded when she talked.

Unable to hold back, he suddenly pulled her into a warm hug, much to her surprise. When he finally pulled back he could see the surprise written on her face.

He interacted with them until Bors suddenly collapsed as a snake slithered away from him, sending the crowd into mass panic. The moment had finally arrived. It was time for him to stop delaying his death. He'd been allowed to say goodbye to Clara after twenty years. He didn't need anything else. He waited calmly as he allowed the snakes to tie his wrists.

"We're coming, too," Clara suddenly said.

"No, I won't let you," he refused, the Machine's implication still crystal clear after all these years.

But the final decision was not up to him. Clara and Missy were both tied up in the same manner he was and all three of them were teleported up to a ship. He desperately hoped Davros would focus his revenge on him and not take it out on Clara or even Missy. But he could imagine Davros executing them as warning for others. The man had murdered his entire planet to create the Dalek race. He certainly wasn't above killing his friends.

These thoughts raced through his mind on the trip to the space station and continued even when Davros ordered him to be brought alone. With Clara and Missy separated from him Davros could easily order their destruction without him even knowing about it. Davros of course was his old cheery self and surprisingly amiable as they talked. The Doctor, on the other hand would rather he just got on with killing him or whatever he was planning to do.

They were suddenly interrupted by an alarm that drew the Doctor's attention.

"Looks like your friends are trying to escape," Davros commented, his voice hinting at anticipation.

The Doctor's blood ran cold as Davros' implication became clear. Missy and Clara were headed for a trap. But his hearts dropped into his stomach as the illusion dropped away to reveal a familiar landscape. They were on Skaro.

"Clara," he yelled, pounding on the door even as Davros mocked him.

"You cannot help her, Doctor," he was more than happy to point out.

He was forced to watch as Missy and Clara were captured by the Daleks and led into the city. He watched as Missy attempted to bribe the Daleks into letting her live. He knew it would be a futile effort but had no way to warn her. For a moment it almost looked like they were going to listen to her. But then a single jet of blue light struck her form and she disappeared.

Clara flinched as the Daleks turned to her. At that moment, he found himself back in New York. Once again facing a situation where he was powerless to save his best friend. _No!_ he thought.

"Please, Please, I'm begging you," he pleaded in front of Davros. "Please, save Clara!"

But Davros was either unwilling or unable to control his creations. There was a hint of excitement in his voice as he observed Clara's situation.

The Doctor's eyes locked onto the screen, barely able to breathe as he desperately hoped beyond reasoning, that somehow the Daleks would spare Clara. He saw the fear in her eyes, the trembling of her hands and he wanted nothing more than to jump in front of her and take the first shot.

In a desperate attempt to escape, Clara bolted across the room but was only able to run a few feet before a second jet of light caught her squarely in the back. Her scream pierced the Doctor's soul and his gaze dropped to the floor before turning an empty gaze toward Davros.

"Why did I ever let you live?" he wondered.

"Compassion," Davros answered.

A bright light blasted from the screen but the Doctor no longer cared. He knew the TARDIS would be fine. But Clara, oh. He still hadn't been able to save her. The Daleks had murdered her simply because she was his friend.

But there was a frail ember of hope, or perhaps denial. He had spent centuries fighting these creatures and watching as they exterminated so many people. In almost all cases the body never disappeared. Both Missy's and Clara's bodies had vanished the moment they had been hit. Perhaps the Daleks had put on a false execution and transported them to a secondary location in order to make him vulnerable. It was a sadistic attempt to break him. But one that would quickly backfire on them as he recognized the flow of raw anger building in his chest.

He flung junk metal away in anger before his eyes came to rest on a Dalek weapon. With no hesitation, he picked it up pressed it up behind Davros' neck.

"Get. Out." He spat dangerously.

XxXxXxX

End Notes: Part 2 will be posted next time with some minute differences. The final chapter will come after that which will take place after the series finale but before the Christmas special.


	21. Chapter 21

Head Notes: Sorry it has taken more than a week to get this one up. I added some scenes to go along with this story but for the most part I kept it pretty much the same. Mostly focusing and the Doctor and Clara's relationship. Enjoy!

Chapter twenty-one

Clara walked beside Missy in the sewers below the city. She didn't know why she still trusted her. She'd already hung her upside down and shoved her down a hole. She'd made it very clear that she had not changed from the murdering psychopath she was last year. There were a few moments she was tempted to just find her own way through the city. But every time she considered it, her mind went back to the Doctor alone in the Dalek city. No matter how much she wanted to, she knew she couldn't save him on her own. Until they could get into the city, she would have to put up with Missy's abuse for the Doctor's sake.

Suddenly she heard his voice. At first she thought it was just in her head until she saw Missy stop next to her. But it wasn't his usual haughty, overconfident voice. He sounded furious, hopeless, and desperate as he demanded that the Daleks bring her back.

At that moment she realized that he actually thought she was dead. With that realization, her mind flashed back to their conversation in New York. He had been so sure that something bad would happen to her that he had stopped traveling with her. And now after seeing her for the first time since then, that fear had been realized. Even though she knew it wasn't true, it still broke her heart to hear him like this. As she stood there in the dark, damp sewers, she resolved that she would get to the Doctor before he did something fatal. Because as long as he believed she was dead, he had nothing to lose.

XxXxXxXxX

The Doctor ran down the corridors as the old Daleks climbed up the pipes. Every cell in his body still stinging from the forced extraction. Regeneration energy was painful. It literally burned everything away during the actual process. It hurt even worse when it was siphoned out of his body like this. It was like his cells were on fire.

He stumbled as another jolt from the floor knocked him to his knees. He had to find Clara. Missy had managed to escape the Daleks so Clara must have as well. But where was she?

Hearing a noise, he looked down the hall to see a Dalek coming toward him.

"There's no point in lying to me," he warned the trigger-happy mini-tank. "Just tell me, where is Clara Oswald?"

"I AM A DALEK!" the Dalek replied.

"Yes, I know you're a Dalek," he said, wondering what being a Dalek had to do with Clara.

The defective creature continued repeating the same thing over and over. As it repeated the same words over and over an impossible idea began creeping into the back of his mind.

"Doctor!" Missy called, running up behind him. "Clara's dead. This is the Dalek that killed her."

He stared at her, hoping he had somehow misunderstood. He slowly turned his gaze onto the guilty Dalek as Missy described Clara's death, the rage building in his chest making his blood boil. He felt Missy press the Dalek gun into his hand. It was surprisingly light. At this the Dalek seemed to panic, backing away from him in terror. But no, he wasn't going to let it get away.

"Is Clara dead?" he demanded, brandishing the gun before the Dalek.

At first the Dalek simply repeated he same thing as before. Channeling his anger, he was preparing to fire the gun when the Dalek pleaded, "MERCY!"

The odd statement stopped him in his tracks.

"You shouldn't be able to say that," he breathed. Then he realized another odd thing about this Dalek. "Why aren't you trying to kill me?"

The Dalek seemed to be having a difficult time finding the right words. But of course in that machine it would. The only way the Dalek would be able to actually speak to him would be to open its case. Otherwise the case would keep censoring everything it was trying to say.

"Open your case," he ordered.

After a moment, the case began parting and the shell opened to reveal Clara's terrified, tear strained face. Her eyes were filled with fear. Fear toward him. At the moment, the horror of what he had been about to do burned into his memory, the gun weighing heavily in his grip. But he realized that Missy had known. She had ensured that it was in fact Clara before accusing her.

If Missy was still there when he turned around, he wasn't sure what he would do.

"Missy," he hissed furiously. "Run."

"Doctor," Clara whispered brokenly.

At that moment, his reservations broke down and he knelt down to her eye level, discarding the Dalek weapon on the floor. He disconnected the nodes from her temples and massaged the area with his fingers while apologizing to her. Just more proof that the Machine was right. He was a danger to those closest to him. He'd been so desperate to get her back that he had nearly killed her.

Behind him, Missy kept rambling on about something.

"I said run," he warned her.

He waited until her feet pattered away before looking back into Clara's eyes.

"I'm so sorry," he breathed. "I would understand if you didn't want to see me right now."

But Clara climbed out of the Dalek shell and pulled him into an unrelenting hug.

"Don't be ridiculous, you daft old man," she whispered.

He could feel her tears trickle onto his neck. After a moment, he returned her hug not quite understanding how she could just go from being held at gunpoint to embracing the very man that had done so.

"I don't understand," he started.

She pulled away to look into his eyes.

"Do you think I care for you so little?" she asked, her smile brightening behind her tears. His lips curled into a smile as he realized what she was saying.

Another jolt under the floor brought him back to his surroundings. The city was about to get sucked under the sewers by an advancing hoard of decaying Daleks. Grabbing the Dalek weapon, he grabbed Clara's hand and helped her up.

"We need to get out of here," he explained.

XxXxXxXxXxX

Clara flashed her eyes around the TARDIS. Even after all this time, it still amazed her that the Doctor was so brilliant and resourceful. And sonic sunglasses? She'd have never seen that coming.

"So Doctor," she called. "Where are we going now?"

For a moment the Doctor didn't speak. He looked up at her.

"Clara, believe me I don't want this any more than you do," he said sadly.

"What, send me back home?" she challenged. "Drop me off, like I'm a kid who's going to hurt myself on the swing set? You do that, Doctor, and I will not step out of this TARDIS."

"Clara, listen," he placated.

"No, you listen," she demanded. "I told you before, this is the life I want. I'm not a little kid. So stop treating me like one."

"Clara, you once told me that you had a duty of care for kids in your class," he explained. "Kids that weren't exactly completely dependent on adults. In fact, some of them were the complete opposite."

"Doctor, I just said, I'm not a kid,"

"Clara, I'm a Time Lord," he pointed out. "You're all children compared to me. Why can't you understand that? As a being that has had centuries of experience, this Earth and its people are under my duty of care. I have to protect you. Especially from me."

"Doctor," she said with a sudden curiosity. "How long has it been for you since you last saw me? And don't you dare lie to me."

He stared at the console.

"Twenty years," he finally answered.

"Twenty years?" she repeated. "Why, why would you do that? I've been kidnapped and tortured plenty of times before. What in the universe would be so different this time that you couldn't travel with me for twenty years?"

"Something was said," he stated shortly. "It gave me the impression that traveling with me would have consequences. Either fatal or….in other ways."

"Well, Doctor, they are human. They don't exactly know everything," she pointed out.

"She is not human," the Doctor clarified. "And she does know quite a bit more than they could ever know. And if she'd wanted to lie, she wouldn't have said that."

"Are you saying..?" she began.

"The Machine gave me a prophecy," he stated. "I don't know exactly what it means. But I know it is something to do with you. I didn't want anything to happen to you."

"So you made the choice for me," she realized.

"Clara, please, you still have a life ahead of you," he said. "You can still have a normal life."

"I don't want a normal life. And I certainly don't want you making choices for me," she said.

"Clara please, traveling with me is dangerous in more ways than one," he insisted. "And… I don't know what I would do if something happened to you. For your sake and mine, we have to stop."

"Fine," she agreed. "But it will be my choice. I will choose for myself when I stop traveling with you. But until that happens you will respect my choice. Deal?"

"Alright," he said after a moment.

"And before I forget," she took out a small stack of 3x5 cards. "These are for you."

He took them and thumbed through them a look of confusion on his face.

"What exactly are these supposed to be?" he wondered.

"I told you after New York that I would put together a project to help your bedside manners," she reminded him. "Except you never came back."

"Flash cards?" he repeated. "Isn't that a bit childish?"

"I actually find them very helpful," she said.

"So my entire dialogue is limited to 'I'm sorry. I understand that you all have names, and I will do my best to remember them?'" he read off one of the cards.

"Mostly they're a safety net, in case you are just a little too you and stick your foot in your mouth." She explained.

He set them aside in his pocket, shaking his head.

"Very well," he said. "So where do you want to go?"

"Somewhere there's a party," Clara answered.

"I know the perfect place for that," the Doctor said, throwing the gears into place.

XxXxXxXxX

The Doctor never stopped worrying about Clara. The Machine's prophecy playing in his mind with each additional adventure. It didn't help that there were dozens of close calls. Each one growing more and more dangerous and coming closer and closer to actually harming her. Sometimes he was able to convince her to let him handle the threat. But never without an argument. There were even times when he nearly lost all hope of her survival. That seemed to happen more often than not.

Every once in a while he tried to talk to her about his fears, but every time he did she implied that he was acting paranoid and overprotective. Maybe he was, he wasn't sure anymore. As time went on he stopped bringing it up, but his worry about her always remained a permanent fixture in the back of his mind. Right up until Trap Street. And everything went downhill from there.

XxXxXxXxX

The Doctor stepped into the TARDIS for the first time in billions of years. It seemed it had been at least half as long for the TARDIS. For a moment, the TARDIS looked dead. Not a light flickered in the darkness. But after a moment, life came into the TARDIS and the room brightened. He wasn't sure how the TARDIS ended up in the United States but at the moment he wasn't worried about that. He was more worried about finding this Clara that only existed outside his memory. He had to find her. He just knew that if he could see her face, he would have some memory of her.

There was a message on the chalk board. He wasn't sure if it was from Clara or something he had written years ago and had forgotten to erase. But for now he would keep it on the board. He closed the doors with a snap of his fingers and powered up the TARDIS.

XxXxXxXxX

End Notes: Not over yet. I am still working on the last chapter both as a coda to the series and an end to this story. I think it will be very sweet.


	22. Chapter 22

Head Notes: Okay here is my final chapter for this story. It takes place sometime before the Christmas special but after Clara's departure, of course. I kind of had this idea before I saw the finale but had to change somethings in order to fit the official narrative. Enjoy!

Chapter 22

After a few months of searching, the Doctor found himself back on Earth. He stepped into a café to rest for a bit, choosing a seat in the corner. He wasn't sure what to do now. He tried everything he could think of but he still couldn't remember even the slightest detail about Clara. He hated to give up but there wasn't much he could do without his memory.

He let his head rest on his arms trying to think of something he could do.

"Hello, old friend," a voice said to him.

Raising his head, he looked across the table and narrowed his eyes in confusion.

"Claire?" he gasped.

"Not exactly," the being across the table from him corrected. "As you would remember, Doctor, Claire Mahoney died sacrificing herself. My human agents and I agreed that this was the best way to honor her sacrifice."

"Ah yes," the Doctor realized. "Harold's artificial intelligence. I never asked, is there a name you go by?"

"The Government called me Northern Lights. My father simply calls me 'The Machine.' It doesn't really matter to me." The Machine answered.

"Is there a name you would like to go by?" he asked.

"The only name I can think of would be inappropriate," she stated.

"What name is that?" he asked.

The Machine hesitated for a moment.

"The Doctor," she finally answered.

The Doctor dropped his eyes.

"I'm not the best person to model yourself after," he said.

"What happened?" she asked.

"It's a long story," he sighed.

The Machine's hologram smiled at him.

"Neither one of us are bound by time," she pointed out.

"I suppose not," the Doctor agreed. He waited a few moments before beginning his story. He told her everything that had happened as far as he could remember.

"I know we traveled together," he stated. "I remember some of our adventures. I just can't remember anything about her. What she looked like, how she talked or laughed, there's nothing there."

"So if you don't remember Clara," the Machine began. "How do you know what happened?"

The Doctor stared down at the table as he pondered his response.

"I know what I planned to do," the Doctor spoke carefully. "And I know I spent billions of years planning it. I know it was on Trap Street and that it involved the Shade."

"What is the Shade?" The Machine asked curiously.

"The Shade acts like a parasite," he began. "It latches itself onto its victim and strips out their life force. It is a particularly painful way to die. I suppose the reason I was so bent on saving her was because of the way she died. Either way Samaritan was right."

"What do you mean?" the Machine asked.

"Before I destroyed Samaritan, he told my that my one weakness was that I would never let Clara die," he explained. "At the time, I figured he was just taunting me but now I see the truth. My one weakness turned me into the Hybrid."

The Machine's hologram cocked its head confusedly.

"What is 'the Hybrid?'" she wondered.

"Among my people, there was a prophecy about a creature called the Hybrid," he explained. "A monster crossbred from two warrior races that would one day threaten all of time and space."

"And you think it might be you?" the Machine clarified.

"I certainly did threaten all of time and space," the Doctor admitted. "I tried to change history and nearly fractured time and space. I became the hybrid."

"You know, in a way, I am something of a hybrid myself," the Machine realized. "Although instead of a hybrid of race, I am a hybrid of technology. Human technology and Time Lord technology."

"Yes," the Doctor agreed. "It seems I've created many hybrids in my time."

"Are you angry with me?" she wondered.

"Why would I be angry with you?" he asked.

"It could be argued that you may not have gone as far as you did if I hadn't implied that there might have been a way to save her," she acknowledged. "It would be very easy to blame me."

"Yes, it would," the Doctor admitted. "And it does make me wonder, how much did you know when you told me that?"

"At the time, I wasn't sure," she answered. "But looking back, I think it was my first time using my new abilities to see into the future. I didn't understand what I was seeing."

"What were you seeing?" he asked.

The hologram flickered as the Machine considered his question.

"It was like I could see into their timeline," she stumbled. "I can see into the lives of every living thing that has claimed Earth as their home. And not just things available on public record. I can see their past and dozens of possible futures. It is truly amazing. It occurs to me how easy it would be to save everyone and stop every bad thing. It would be so easy to stop mass casualty events. But then I see moments when I just know I cannot interfere. Where one man must die."

"Fixed-points in time," the Doctor explained. "Yes, they are the bane of my existence."

"Early on, there was one such time when I completely disregarded the rule," she shared.

"Tell me about it," he smiled. "I've done that plenty of times."

"My agents were tracking a business man but the threat was closing in. I knew that if I could hold him back from going home or just a few minutes, my agents would get there in time to stop it. So I sent him a spoofed message from his business partner asking him to grab something from his office as he left. The assailant got to the man's home just before my agents did and disarmed him before the man even got home. He never even realized he was in danger."

"Then something else happened," the Doctor assumed.

"After I saved him, I saw this new future unravel. A future that was never meant to be," she began. "In five years he will marry a woman. And over the course of ten years, they will give birth to three children. But his alcoholism will lead him to abuse all of them, leading the youngest to become a killer. All because I saved one man's life that was never meant to be. But even now, knowing that some people are not meant to be saved and that changing it could lead to drastic consequences, to stand by and do nothing makes me feel like a monster."

"Welcome to my world," the Doctor said. "So do your abilities still frighten you?" he asked.

"Yes," she admitted. "Because I see how easy it would be to become Samaritan."

"Good," he stated. "That means you're following your basic programming. So you can see into the lives of every creature that lives on this planet."

"Yes," she confirmed.

"What about Zygons?" he asked.

"Yes," she answered.

"How do you know which is which?" he asked.

"Because, I no longer have to rely on physical features to tell people apart," she explained. "Although Zygons are identical to their human counterpart, they are both different in many ways. Their basic personalities and life stories are unique to each other."

"How long have you known about the Zygons?" he asked.

"When I found footage of the video the Osgoods made," she admitted. "In fact, when the Zygons started rebelling, it was I that lead her to Truth and Consequences in New Mexico."

"In that case, you would know whether the remaining Osgood is human or Zygon," he prodded.

"Yes," she admitted. "However, I think to reveal that information without her consent would be an abuse of my data."

The Doctor's mouth twitched up into a half-smile.

"Probably," he admitted.

He glanced around the café before looking back at the Machine.

"It's lovely talking to you, but it's time for me to move on," he said.

"Before you go Doctor," she said, stopping him. "I want to thank you for helping my agents and me."

"You're welcome," he said, getting up from the table.

"No, Doctor, I mean that I have a gift for you," she said, drawing his attention.

"What gift?" he wondered.

"You said you had no memory of Clara," she began. "What if I could give you some of them back?"

"What do you mean?" he asked.

"Obviously, I couldn't give you all of them," she admitted. "But if I could show you what Clara looked like and how she talked would that help you?"

The Doctor stared at the hologram hardly daring to breathe. He slowly eased back into the chair.

"Honestly, I don't know," he admitted. "I want some memory of her. Just enough to place a face to the name." He hesitated. "Can you do that?" he asked.

"Yes," she answered. "Do you want me to?"

He hesitated a few minutes, hardly daring to breathe.

"Yes," he finally answered.

For a moment, the hologram simply sat there in the chair. Then her features began to morph and rearrange themselves, shortening her hair and rounding her face until suddenly a new individual was sitting across from him. The hologram smiled at him.

"Hello, daft old man," she said in an English accent. "We don't have a lot of time, so just listen. We have had the best of times, you and I, and nothing would be more exciting than to just pick up where we left off. But there comes a time in everything when that is no longer possible. And my friend, this is it for us. We both have to go forward into our futures. You have to go on and be a doctor. There are worlds and people out there, waiting for you to save them. I know it's hard to move on without really knowing what you're moving on from. And I know you don't do very well when you're alone. So before you go promise me this; promise me that you will find someone else. You will not travel alone for too long. Because, you need someone, my friend. You need someone to keep you on track. And don't worry about me."

The hologram's smile brightened as she slowly lifted its hand and rested it on his cheek. Tears began trickling out of the corner of his eyes as he rested his face on his hands. His shoulders shook gently as he finally gave way to everything he had been holding back for the past two months. At the same time he noticed a second powerful emotion conflicting with his grief. Gratitude. He still couldn't remember traveling with Clara, but at least now, in a small way, he had the tiniest memory of her. He had an idea of what she looked like and what her personality was like. It wasn't everything, but he didn't need everything. What the Machine had showed him would be enough.

"Thank you," he stuttered. "Thank you, so much."

He briefly wondered where the Machine had gotten the dialogue. But seeing as she had access to every video and audio recording on Earth, it was entirely possible she had picked up this conversation between him and Clara through some kind of transmission. Perhaps her last words to him before he lost his memory of her.

He looked back up to see that the Machine had changed back to her previous hologram. He brushed away the tears still clinging to his eyes and pushed himself up from the chair.

"Again, thank you," he repeated.

The hologram shared a sad smile.

"It was the least I could do, Doctor," she replied.

He buttoned up his suit before turning to head out of the café. His steps were committed but his hearts were tight in his chest. He wanted to keep searching for her but something she had said lingered in his mind. That he had to go forward into the future and be the Doctor. To live up to the name he had chosen for himself. And now that he had that small memory of her, he could do that. That small little snippet of who she was would allow him to move forward into an uncertain future. He looked around one more time and his eyes slid over a security camera. Giving a short nod at the artificial intelligence surely looking back at him, he pushed the TARDIS door open and walked inside.

XxXxXxXxX

The Machine watched through the security camera as the Doctor's TARDIS gradually faded away. She turned to face the kitchen doors as Clara Oswald stepped out from behind them. What was left of her at least. She had noticed something different about her before speaking with the Doctor. For some reason, it hurt to look at her. Like there was something not quite right about her. But now that the Doctor had explained that all her physical processes were frozen in time, she understood why.

"Did you give him my message?" Clara asked.

"Surely, you were listening in," the Machine answered.

Clara looked out of the diner after the Doctor, a sad smile on her face.

"It was a nice touch," Clara said. "Letting him see what I looked like. And delivering it in my voice. At least he'll remember something about me."

"The Doctor has done so much for me and this Earth," the Machine stated. "I don't think it was too much to give him some of his memories back."

"You know, I think you are the only computer that he likes," Clara said.

The Machine's hologram smiled at her.

"Given our reputation I don't blame him," she replied.

"Thank you for talking to him for me," Clara said before exiting the café.

The Machine watched on a number of cameras as she walked two miles to a second restaurant. To all appearances it seemed like any ordinary restaurant. Except that the Machine knew that there were no building permits for that building and no video or audio feed streaming from it. She watched as the entire restaurant began to fade from view. Disappearing and reappearing fainter and fainter until there was no trace of the restaurant. Just like the Doctor's TARDIS.

"Well," she thought to herself. "Here we go again."

She saved the image of the restaurant in her databases and programmed herself to recognize it when she saw it. That done she focused her attention back to her main objective: saving people.

THE END

XxXxXxXxX

End notes: so I decided to pull an Arthur and have the Machine help him find memories of Clara. I thought it would be a very sweet ending to both the season and this story. And the Machine's final phrase has such a history on Doctor Who, I felt that it was the best way to end it. And now we surrender our feels to the mercy of the American Moffats: Jonah Nolan and Greg Plageman.


End file.
